Starting phenix.real_space_refine on Fri Aug 22 13:02:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ws9_37802/08_2025/8ws9_37802.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ws9_37802/08_2025/8ws9_37802.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ws9_37802/08_2025/8ws9_37802.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ws9_37802/08_2025/8ws9_37802.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ws9_37802/08_2025/8ws9_37802.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ws9_37802/08_2025/8ws9_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-2.0-5787/lib/python3.9/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: 1.10, per 1000 atoms: 0.38 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: 0.39 Conformation dependent library (CDL) restraints added in 80.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.37 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: 0.43 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 677 1.33 - 1.45: 871 1.45 - 1.57: 1452 1.57 - 1.69: 99 1.69 - 1.81: 4 Bond restraints: 3103 Sorted by residual: bond pdb=" CA ARG A 70 " pdb=" C ARG A 70 " ideal model delta sigma weight residual 1.517 1.557 -0.041 1.02e-02 9.61e+03 1.58e+01 bond pdb=" C ARG A 70 " pdb=" N PRO A 71 " ideal model delta sigma weight residual 1.332 1.373 -0.041 1.33e-02 5.65e+03 9.63e+00 bond pdb=" CA SER A 336 " pdb=" C SER A 336 " ideal model delta sigma weight residual 1.525 1.497 0.028 1.28e-02 6.10e+03 4.70e+00 bond pdb=" N PRO A 324 " pdb=" CA PRO A 324 " ideal model delta sigma weight residual 1.469 1.445 0.024 1.28e-02 6.10e+03 3.43e+00 bond pdb=" N ASN A 99 " pdb=" CA ASN A 99 " ideal model delta sigma weight residual 1.457 1.478 -0.020 1.29e-02 6.01e+03 2.47e+00 ... (remaining 3098 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 4046 1.15 - 2.31: 295 2.31 - 3.46: 63 3.46 - 4.62: 19 4.62 - 5.77: 5 Bond angle restraints: 4428 Sorted by residual: angle pdb=" N LYS A 302 " pdb=" CA LYS A 302 " pdb=" C LYS A 302 " ideal model delta sigma weight residual 114.75 110.65 4.10 1.26e+00 6.30e-01 1.06e+01 angle pdb=" C3' C B -8 " pdb=" O3' C B -8 " pdb=" P G B -7 " ideal model delta sigma weight residual 120.20 124.88 -4.68 1.50e+00 4.44e-01 9.72e+00 angle pdb=" N SER A 105 " pdb=" CA SER A 105 " pdb=" C SER A 105 " ideal model delta sigma weight residual 110.24 114.76 -4.52 1.47e+00 4.63e-01 9.45e+00 angle pdb=" N ASN A 130 " pdb=" CA ASN A 130 " pdb=" C ASN A 130 " ideal model delta sigma weight residual 113.38 109.63 3.75 1.23e+00 6.61e-01 9.31e+00 angle pdb=" CA ARG A 70 " pdb=" C ARG A 70 " pdb=" O ARG A 70 " ideal model delta sigma weight residual 120.94 117.98 2.96 1.01e+00 9.80e-01 8.61e+00 ... (remaining 4423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.22: 1622 34.22 - 68.44: 201 68.44 - 102.66: 13 102.66 - 136.88: 1 136.88 - 171.10: 2 Dihedral angle restraints: 1839 sinusoidal: 1174 harmonic: 665 Sorted by residual: dihedral pdb=" O4' U B -9 " pdb=" C1' U B -9 " pdb=" N1 U B -9 " pdb=" C2 U B -9 " ideal model delta sinusoidal sigma weight residual 232.00 72.61 159.39 1 1.70e+01 3.46e-03 6.43e+01 dihedral pdb=" C4' DG D -8 " pdb=" C3' DG D -8 " pdb=" O3' DG D -8 " pdb=" P DG D -7 " ideal model delta sinusoidal sigma weight residual -140.00 31.10 -171.10 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' C B -8 " pdb=" C3' C B -8 " pdb=" O3' C B -8 " pdb=" P G B -7 " ideal model delta sinusoidal sigma weight residual -110.00 15.71 -125.71 1 3.50e+01 8.16e-04 1.24e+01 ... (remaining 1836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 433 0.058 - 0.116: 60 0.116 - 0.174: 13 0.174 - 0.232: 1 0.232 - 0.290: 1 Chirality restraints: 508 Sorted by residual: chirality pdb=" CA ASN A 99 " pdb=" N ASN A 99 " pdb=" C ASN A 99 " pdb=" CB ASN A 99 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA ARG A 345 " pdb=" N ARG A 345 " pdb=" C ARG A 345 " pdb=" CB ARG A 345 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.91e-01 chirality pdb=" CA ARG A 70 " pdb=" N ARG A 70 " pdb=" C ARG A 70 " pdb=" CB ARG A 70 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.86e-01 ... (remaining 505 not shown) Planarity restraints: 380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 75 " 0.050 5.00e-02 4.00e+02 7.46e-02 8.90e+00 pdb=" N PRO A 76 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 71 " -0.014 2.00e-02 2.50e+03 2.73e-02 7.45e+00 pdb=" C PRO A 71 " 0.047 2.00e-02 2.50e+03 pdb=" O PRO A 71 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU A 72 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B -1 " -0.024 2.00e-02 2.50e+03 1.21e-02 4.01e+00 pdb=" N9 A B -1 " 0.030 2.00e-02 2.50e+03 pdb=" C8 A B -1 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A B -1 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A B -1 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A B -1 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A B -1 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A B -1 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A B -1 " 0.000 2.00e-02 2.50e+03 pdb=" N3 A B -1 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A B -1 " -0.001 2.00e-02 2.50e+03 ... (remaining 377 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 577 2.78 - 3.31: 2625 3.31 - 3.84: 5096 3.84 - 4.37: 5917 4.37 - 4.90: 8839 Nonbonded interactions: 23054 Sorted by model distance: nonbonded pdb=" O TYR A 317 " pdb=" N2 G B -20 " model vdw 2.245 3.120 nonbonded pdb=" NH2 ARG A 260 " pdb=" OP2 U B -17 " model vdw 2.307 3.120 nonbonded pdb=" ND2 ASN A 195 " pdb=" O2' C B 4 " model vdw 2.309 3.120 nonbonded pdb=" NZ LYS A 259 " pdb=" OP2 A B -3 " model vdw 2.330 3.120 nonbonded pdb=" ND2 ASN A 138 " pdb=" OP2 DG C -2 " model vdw 2.348 3.120 ... (remaining 23049 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.680 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.920 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5711 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 3103 Z= 0.223 Angle : 0.718 5.769 4428 Z= 0.437 Chirality : 0.045 0.290 508 Planarity : 0.007 0.075 380 Dihedral : 23.810 171.102 1413 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 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 aren 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 covalent geometry : bond 0.00395 ( 3103) covalent geometry : angle 0.71790 ( 4428) hydrogen bonds : bond 0.21555 ( 82) hydrogen bonds : angle 7.77513 ( 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 : 0.082 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: 0.1367 time to fit residues: 4.6938 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 : 0.080 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 13 optimal weight: 0.3980 chunk 1 optimal weight: 0.0870 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 135 HIS ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.196865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.175384 restraints weight = 4785.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.179446 restraints weight = 2771.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.182306 restraints weight = 1861.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.184192 restraints weight = 1384.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.185705 restraints weight = 1111.462| |-----------------------------------------------------------------------------| r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5699 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3103 Z= 0.184 Angle : 0.659 6.387 4428 Z= 0.349 Chirality : 0.039 0.147 508 Planarity : 0.007 0.043 380 Dihedral : 26.526 170.745 958 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.73 % Favored : 89.82 % Rotamer: Outliers : 2.01 % Allowed : 9.55 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.55), residues: 226 helix: -1.38 (0.60), residues: 65 sheet: 0.75 (1.18), residues: 24 loop : -1.38 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 314 TYR 0.007 0.001 TYR A 87 PHE 0.007 0.001 PHE A 350 TRP 0.018 0.002 TRP A 304 HIS 0.002 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 3103) covalent geometry : angle 0.65889 ( 4428) hydrogen bonds : bond 0.09151 ( 82) hydrogen bonds : angle 5.62834 ( 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 26 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.085 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 25 average time/residue: 0.1289 time to fit residues: 3.6443 Evaluate side-chains 25 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.092 ------------------------------------------------------------------------------- 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: 0.9980 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 0.1980 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 135 HIS A 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 = 0.4384 r_free = 0.4384 target = 0.192309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.170584 restraints weight = 4649.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.174760 restraints weight = 2555.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.177689 restraints weight = 1652.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.179716 restraints weight = 1200.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.180963 restraints weight = 944.581| |-----------------------------------------------------------------------------| r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5764 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3103 Z= 0.203 Angle : 0.679 5.993 4428 Z= 0.356 Chirality : 0.039 0.145 508 Planarity : 0.006 0.038 380 Dihedral : 26.562 170.928 954 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.73 % Favored : 89.82 % Rotamer: Outliers : 2.51 % Allowed : 12.56 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.56), residues: 226 helix: -1.51 (0.61), residues: 65 sheet: 0.96 (1.21), residues: 24 loop : -1.47 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 276 TYR 0.007 0.001 TYR A 199 PHE 0.007 0.001 PHE A 350 TRP 0.023 0.003 TRP A 304 HIS 0.002 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 3103) covalent geometry : angle 0.67889 ( 4428) hydrogen bonds : bond 0.08996 ( 82) hydrogen bonds : angle 5.32863 ( 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 31 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.082 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 29 average time/residue: 0.1067 time to fit residues: 3.5159 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 : 0.081 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 349 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.190338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.168359 restraints weight = 4626.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.172515 restraints weight = 2564.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.175394 restraints weight = 1676.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.177412 restraints weight = 1232.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.178590 restraints weight = 978.218| |-----------------------------------------------------------------------------| r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5794 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3103 Z= 0.202 Angle : 0.682 6.347 4428 Z= 0.360 Chirality : 0.039 0.143 508 Planarity : 0.006 0.039 380 Dihedral : 26.547 171.111 954 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.62 % Favored : 88.94 % Rotamer: Outliers : 3.52 % Allowed : 14.07 % 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 aren not related in a simple way. whole: -1.77 (0.57), residues: 226 helix: -1.56 (0.60), residues: 65 sheet: 1.10 (1.27), residues: 24 loop : -1.43 (0.55), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 276 TYR 0.008 0.002 TYR A 199 PHE 0.007 0.001 PHE A 350 TRP 0.022 0.003 TRP A 304 HIS 0.002 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 3103) covalent geometry : angle 0.68158 ( 4428) hydrogen bonds : bond 0.08760 ( 82) hydrogen bonds : angle 5.13365 ( 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 35 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.083 Fit side-chains REVERT: A 277 LYS cc_start: 0.7885 (mmmm) cc_final: 0.7437 (ttmm) REVERT: A 310 ARG cc_start: 0.6532 (mtm180) cc_final: 0.5969 (mtm180) outliers start: 7 outliers final: 3 residues processed: 33 average time/residue: 0.1203 time to fit residues: 4.4589 Evaluate side-chains 29 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 120 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.0870 chunk 8 optimal weight: 0.2980 chunk 4 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.191032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.169420 restraints weight = 4543.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.173569 restraints weight = 2495.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.176532 restraints weight = 1614.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.178600 restraints weight = 1163.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.180012 restraints weight = 912.094| |-----------------------------------------------------------------------------| r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5759 moved from start: 0.2632 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= 0.176 Angle : 0.663 6.028 4428 Z= 0.347 Chirality : 0.039 0.160 508 Planarity : 0.006 0.038 380 Dihedral : 26.502 172.220 954 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.73 % Favored : 89.82 % Rotamer: Outliers : 3.02 % Allowed : 15.58 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.57), residues: 226 helix: -1.35 (0.62), residues: 65 sheet: 1.00 (1.27), residues: 24 loop : -1.37 (0.55), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 276 TYR 0.008 0.001 TYR A 87 PHE 0.006 0.001 PHE A 350 TRP 0.024 0.003 TRP A 304 HIS 0.002 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 3103) covalent geometry : angle 0.66262 ( 4428) hydrogen bonds : bond 0.08811 ( 82) hydrogen bonds : angle 4.92860 ( 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 33 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.087 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 30 average time/residue: 0.1077 time to fit residues: 3.6773 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 : 0.085 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 1 optimal weight: 0.0870 chunk 8 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 5 optimal weight: 0.2980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 135 HIS ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.192209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.170609 restraints weight = 4577.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.174829 restraints weight = 2502.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.177821 restraints weight = 1609.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.179568 restraints weight = 1157.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.181187 restraints weight = 925.212| |-----------------------------------------------------------------------------| r_work (final): 0.4259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5730 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3103 Z= 0.161 Angle : 0.646 5.911 4428 Z= 0.337 Chirality : 0.038 0.159 508 Planarity : 0.006 0.039 380 Dihedral : 26.428 172.950 954 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.73 % Favored : 89.82 % Rotamer: Outliers : 4.02 % Allowed : 15.58 % 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 aren not related in a simple way. whole: -1.50 (0.57), residues: 226 helix: -1.03 (0.62), residues: 65 sheet: 0.86 (1.24), residues: 24 loop : -1.35 (0.55), 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 87 PHE 0.005 0.001 PHE A 350 TRP 0.025 0.003 TRP A 304 HIS 0.001 0.000 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 3103) covalent geometry : angle 0.64635 ( 4428) hydrogen bonds : bond 0.08296 ( 82) hydrogen bonds : angle 4.69040 ( 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 36 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.082 Fit side-chains REVERT: A 62 LYS cc_start: 0.7746 (tppt) cc_final: 0.7459 (mmmm) REVERT: A 113 PHE cc_start: 0.6636 (OUTLIER) cc_final: 0.5820 (t80) REVERT: A 310 ARG cc_start: 0.6408 (mtm180) cc_final: 0.6050 (mtm180) outliers start: 8 outliers final: 3 residues processed: 32 average time/residue: 0.1297 time to fit residues: 4.6577 Evaluate side-chains 32 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 349 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 1 optimal weight: 0.0070 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.0980 chunk 20 optimal weight: 0.0670 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 135 HIS ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.195035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.173361 restraints weight = 4673.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.177584 restraints weight = 2583.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.180547 restraints weight = 1660.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.182660 restraints weight = 1195.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.184079 restraints weight = 928.293| |-----------------------------------------------------------------------------| r_work (final): 0.4298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5664 moved from start: 0.3000 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 : 0.609 6.276 4428 Z= 0.318 Chirality : 0.037 0.146 508 Planarity : 0.006 0.042 380 Dihedral : 26.369 173.696 953 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.85 % Favored : 90.71 % Rotamer: Outliers : 3.52 % Allowed : 15.58 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.58), residues: 226 helix: -0.69 (0.64), residues: 65 sheet: -0.18 (1.12), residues: 31 loop : -1.05 (0.58), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 314 TYR 0.012 0.001 TYR A 317 PHE 0.005 0.001 PHE A 352 TRP 0.027 0.003 TRP A 304 HIS 0.001 0.000 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 3103) covalent geometry : angle 0.60860 ( 4428) hydrogen bonds : bond 0.07244 ( 82) hydrogen bonds : angle 4.38486 ( 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 38 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.080 Fit side-chains revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7713 (tppt) cc_final: 0.7445 (mmmm) REVERT: A 113 PHE cc_start: 0.6500 (OUTLIER) cc_final: 0.5601 (t80) REVERT: A 310 ARG cc_start: 0.6298 (mtm180) cc_final: 0.5939 (mtm180) outliers start: 7 outliers final: 3 residues processed: 35 average time/residue: 0.1214 time to fit residues: 4.7530 Evaluate side-chains 33 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 308 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 chunk 20 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN A 99 ASN A 135 HIS ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.191385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.169856 restraints weight = 4682.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.173881 restraints weight = 2606.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.176817 restraints weight = 1695.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.178884 restraints weight = 1225.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.180122 restraints weight = 958.239| |-----------------------------------------------------------------------------| r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5743 moved from start: 0.3232 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= 0.189 Angle : 0.678 6.402 4428 Z= 0.352 Chirality : 0.039 0.142 508 Planarity : 0.006 0.037 380 Dihedral : 26.365 173.812 953 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.62 % Favored : 88.94 % Rotamer: Outliers : 3.52 % Allowed : 17.09 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.57), residues: 226 helix: -0.85 (0.62), residues: 65 sheet: 0.55 (1.20), residues: 24 loop : -1.22 (0.56), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 276 TYR 0.007 0.001 TYR A 199 PHE 0.007 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 covalent geometry : bond 0.00416 ( 3103) covalent geometry : angle 0.67822 ( 4428) hydrogen bonds : bond 0.06538 ( 82) hydrogen bonds : angle 4.62924 ( 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 35 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.080 Fit side-chains revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7769 (tppt) cc_final: 0.7462 (mmmm) REVERT: A 109 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6971 (mm) REVERT: A 113 PHE cc_start: 0.6824 (OUTLIER) cc_final: 0.6005 (t80) REVERT: A 310 ARG cc_start: 0.6443 (mtm180) cc_final: 0.6040 (mtm180) outliers start: 7 outliers final: 3 residues processed: 32 average time/residue: 0.1145 time to fit residues: 4.1248 Evaluate side-chains 33 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 349 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 17 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 0.0030 chunk 20 optimal weight: 0.0470 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 0.0050 chunk 22 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 0.8980 overall best weight: 0.2502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 135 HIS ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.195618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.173921 restraints weight = 4788.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.177993 restraints weight = 2727.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.180784 restraints weight = 1802.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.182807 restraints weight = 1326.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.184339 restraints weight = 1048.554| |-----------------------------------------------------------------------------| r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5660 moved from start: 0.3338 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= 0.135 Angle : 0.628 6.747 4428 Z= 0.328 Chirality : 0.037 0.160 508 Planarity : 0.006 0.040 380 Dihedral : 26.270 174.348 953 Min Nonbonded Distance : 2.501 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 aren not related in a simple way. whole: -1.14 (0.58), residues: 226 helix: -0.56 (0.64), residues: 65 sheet: 0.78 (1.25), residues: 24 loop : -1.15 (0.57), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 345 TYR 0.012 0.001 TYR A 317 PHE 0.005 0.001 PHE A 352 TRP 0.028 0.003 TRP A 304 HIS 0.001 0.000 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 3103) covalent geometry : angle 0.62765 ( 4428) hydrogen bonds : bond 0.06033 ( 82) hydrogen bonds : angle 4.37206 ( 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 31 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.087 Fit side-chains revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7776 (tppt) cc_final: 0.7457 (mmmm) REVERT: A 113 PHE cc_start: 0.6619 (OUTLIER) cc_final: 0.5702 (t80) REVERT: A 277 LYS cc_start: 0.7846 (mmmm) cc_final: 0.7499 (ttmm) REVERT: A 310 ARG cc_start: 0.6343 (mtm180) cc_final: 0.6039 (mtm180) outliers start: 5 outliers final: 3 residues processed: 29 average time/residue: 0.1116 time to fit residues: 3.6320 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 : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ARG Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 115 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 9 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 21 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 chunk 4 optimal weight: 0.4980 chunk 12 optimal weight: 0.0270 chunk 7 optimal weight: 0.8980 chunk 1 optimal weight: 0.0670 overall best weight: 0.1576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 135 HIS A 258 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.198804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.177101 restraints weight = 4828.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.181111 restraints weight = 2776.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.183997 restraints weight = 1857.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.186044 restraints weight = 1367.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.187206 restraints weight = 1083.968| |-----------------------------------------------------------------------------| r_work (final): 0.4342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5599 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3103 Z= 0.122 Angle : 0.588 7.108 4428 Z= 0.307 Chirality : 0.036 0.156 508 Planarity : 0.006 0.041 380 Dihedral : 26.181 175.299 953 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.73 % Favored : 89.82 % Rotamer: Outliers : 3.02 % Allowed : 19.60 % Favored : 77.39 % 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 aren not related in a simple way. whole: -0.85 (0.59), residues: 226 helix: -0.10 (0.66), residues: 65 sheet: 0.88 (1.26), residues: 24 loop : -1.09 (0.57), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 345 TYR 0.013 0.001 TYR A 317 PHE 0.004 0.001 PHE A 350 TRP 0.024 0.002 TRP A 304 HIS 0.001 0.000 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 3103) covalent geometry : angle 0.58811 ( 4428) hydrogen bonds : bond 0.06029 ( 82) hydrogen bonds : angle 4.12180 ( 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 35 residues out of total 200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.048 Fit side-chains revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7780 (tppt) cc_final: 0.7482 (mmmm) REVERT: A 113 PHE cc_start: 0.6424 (OUTLIER) cc_final: 0.5432 (t80) REVERT: A 302 LYS cc_start: 0.7668 (ttpp) cc_final: 0.7204 (ttpp) REVERT: A 310 ARG cc_start: 0.6155 (mtm180) cc_final: 0.5865 (mtm180) outliers start: 6 outliers final: 2 residues processed: 33 average time/residue: 0.1439 time to fit residues: 5.2002 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 109 LEU Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 115 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 11 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 chunk 4 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN A 135 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.192632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.170650 restraints weight = 4730.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.174670 restraints weight = 2721.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.177514 restraints weight = 1810.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.179561 restraints weight = 1343.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.181112 restraints weight = 1064.652| |-----------------------------------------------------------------------------| r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5723 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3103 Z= 0.186 Angle : 0.658 7.372 4428 Z= 0.343 Chirality : 0.038 0.153 508 Planarity : 0.006 0.037 380 Dihedral : 26.220 175.076 949 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.50 % Favored : 88.05 % 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 aren not related in a simple way. whole: -1.06 (0.57), residues: 226 helix: -0.20 (0.64), residues: 65 sheet: 0.79 (1.25), residues: 24 loop : -1.26 (0.55), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 276 TYR 0.009 0.001 TYR A 87 PHE 0.008 0.001 PHE A 113 TRP 0.023 0.003 TRP A 304 HIS 0.002 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 3103) covalent geometry : angle 0.65783 ( 4428) hydrogen bonds : bond 0.05964 ( 82) hydrogen bonds : angle 4.42319 ( 178) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 742.49 seconds wall clock time: 13 minutes 18.87 seconds (798.87 seconds total)