Starting phenix.real_space_refine on Thu Jul 2 09:04:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xht_33198/07_2026/7xht_33198.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xht_33198/07_2026/7xht_33198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xht_33198/07_2026/7xht_33198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xht_33198/07_2026/7xht_33198.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7xht_33198/07_2026/7xht_33198.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xht_33198/07_2026/7xht_33198.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xht_33198/07_2026/7xht_33198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xht_33198/07_2026/7xht_33198.map" } resolution = 2.55 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= 0.177 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: 6 Type Number sf(0) Gaussians P 220 5.49 5 Mg 2 5.21 5 S 19 5.16 5 C 4108 2.51 5 N 1449 2.21 5 O 2041 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7839 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 3822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 3822 Classifications: {'RNA': 179} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 12, 'rna3p_pur': 84, 'rna3p_pyr': 69} Link IDs: {'rna2p': 26, 'rna3p': 152} Chain breaks: 3 Chain: "C" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 595 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "D" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 249 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 3155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3155 Classifications: {'peptide': 395} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 376} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 17 Unusual residues: {' MG': 1, 'LDA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.30, per 1000 atoms: 0.17 Number of scatterers: 7839 At special positions: 0 Unit cell: (85.49, 110.39, 130.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 19 16.00 P 220 15.00 Mg 2 11.99 O 2041 8.00 N 1449 7.00 C 4108 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: 0.69 Conformation dependent library (CDL) restraints added in 255.4 milliseconds 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 740 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 6 sheets defined 32.9% alpha, 21.0% beta 82 base pairs and 138 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 20 through 30 Processing helix chain 'A' and resid 89 through 109 removed outlier: 4.419A pdb=" N LYS A 93 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 122 Processing helix chain 'A' and resid 164 through 185 removed outlier: 3.670A pdb=" N VAL A 178 " --> pdb=" O HIS A 174 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 315 Proline residue: A 305 - end of helix Processing helix chain 'A' and resid 324 through 335 Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 342 through 349 Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 409 through 417 Processing helix chain 'A' and resid 418 through 424 Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 8 removed outlier: 6.254A pdb=" N TYR A 6 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU A 45 " --> pdb=" O TYR A 6 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE A 8 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR A 42 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 319 through 323 removed outlier: 3.532A pdb=" N PHE A 80 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR A 73 " --> pdb=" O SER A 78 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER A 78 " --> pdb=" O THR A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 132 Processing sheet with id=AA4, first strand: chain 'A' and resid 379 through 381 removed outlier: 6.375A pdb=" N GLN A 433 " --> pdb=" O HIS A 380 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 393 through 396 removed outlier: 6.752A pdb=" N TYR A 388 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 477 through 479 removed outlier: 6.789A pdb=" N VAL A 467 " --> pdb=" O ARG A 462 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ARG A 462 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE A 445 " --> pdb=" O LEU A 486 " (cutoff:3.500A) 132 hydrogen bonds defined for protein. 375 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 208 hydrogen bonds 388 hydrogen bond angles 0 basepair planarities 82 basepair parallelities 138 stacking parallelities Total time for adding SS restraints: 1.50 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1283 1.33 - 1.45: 3178 1.45 - 1.57: 3525 1.57 - 1.69: 434 1.69 - 1.81: 29 Bond restraints: 8449 Sorted by residual: bond pdb=" N1 LDA A 501 " pdb=" O1 LDA A 501 " ideal model delta sigma weight residual 1.354 1.249 0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" C3' DG C -9 " pdb=" C2' DG C -9 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.93e+00 bond pdb=" C3' DT C -4 " pdb=" C2' DT C -4 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.72e+00 bond pdb=" C3' DA D 2 " pdb=" C2' DA D 2 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.35e+00 bond pdb=" C1 LDA A 501 " pdb=" N1 LDA A 501 " ideal model delta sigma weight residual 1.503 1.454 0.049 2.00e-02 2.50e+03 6.03e+00 ... (remaining 8444 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.36: 12431 5.36 - 10.72: 10 10.72 - 16.08: 2 16.08 - 21.44: 1 21.44 - 26.80: 1 Bond angle restraints: 12445 Sorted by residual: angle pdb=" O3' DT C 10 " pdb=" P DT C 11 " pdb=" OP1 DT C 11 " ideal model delta sigma weight residual 108.00 81.20 26.80 3.00e+00 1.11e-01 7.98e+01 angle pdb=" O3' DT C 10 " pdb=" P DT C 11 " pdb=" O5' DT C 11 " ideal model delta sigma weight residual 104.00 115.97 -11.97 1.50e+00 4.44e-01 6.36e+01 angle pdb=" O3' DT C 11 " pdb=" P DA C 12 " pdb=" OP1 DA C 12 " ideal model delta sigma weight residual 108.00 89.06 18.94 3.00e+00 1.11e-01 3.99e+01 angle pdb=" C3' DT C 11 " pdb=" O3' DT C 11 " pdb=" P DA C 12 " ideal model delta sigma weight residual 120.20 110.80 9.40 1.50e+00 4.44e-01 3.93e+01 angle pdb=" O3' DT C 11 " pdb=" P DA C 12 " pdb=" O5' DA C 12 " ideal model delta sigma weight residual 104.00 113.30 -9.30 1.50e+00 4.44e-01 3.84e+01 ... (remaining 12440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.65: 4368 33.65 - 67.30: 211 67.30 - 100.95: 5 100.95 - 134.60: 0 134.60 - 168.25: 2 Dihedral angle restraints: 4586 sinusoidal: 3437 harmonic: 1149 Sorted by residual: dihedral pdb=" O4' U B 92 " pdb=" C1' U B 92 " pdb=" N1 U B 92 " pdb=" C2 U B 92 " ideal model delta sinusoidal sigma weight residual 232.00 94.55 137.45 1 1.70e+01 3.46e-03 5.77e+01 dihedral pdb=" C4' G B 76 " pdb=" C3' G B 76 " pdb=" O3' G B 76 " pdb=" P A B 77 " ideal model delta sinusoidal sigma weight residual 220.00 51.75 168.25 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" CA ASN A 148 " pdb=" C ASN A 148 " pdb=" N LYS A 149 " pdb=" CA LYS A 149 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 4583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1361 0.056 - 0.112: 154 0.112 - 0.168: 13 0.168 - 0.224: 0 0.224 - 0.280: 1 Chirality restraints: 1529 Sorted by residual: chirality pdb=" CB ILE A 146 " pdb=" CA ILE A 146 " pdb=" CG1 ILE A 146 " pdb=" CG2 ILE A 146 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C1' A B 81 " pdb=" O4' A B 81 " pdb=" C2' A B 81 " pdb=" N9 A B 81 " both_signs ideal model delta sigma weight residual False 2.46 2.30 0.15 2.00e-01 2.50e+01 5.84e-01 chirality pdb=" C3' G B 76 " pdb=" C4' G B 76 " pdb=" O3' G B 76 " pdb=" C2' G B 76 " both_signs ideal model delta sigma weight residual False -2.48 -2.34 -0.14 2.00e-01 2.50e+01 4.96e-01 ... (remaining 1526 not shown) Planarity restraints: 776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B 51 " 0.030 2.00e-02 2.50e+03 1.30e-02 4.66e+00 pdb=" N9 A B 51 " -0.027 2.00e-02 2.50e+03 pdb=" C8 A B 51 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A B 51 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A B 51 " -0.004 2.00e-02 2.50e+03 pdb=" C6 A B 51 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A B 51 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A B 51 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A B 51 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A B 51 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A B 51 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B -8 " -0.028 2.00e-02 2.50e+03 1.41e-02 4.45e+00 pdb=" N1 C B -8 " 0.029 2.00e-02 2.50e+03 pdb=" C2 C B -8 " 0.004 2.00e-02 2.50e+03 pdb=" O2 C B -8 " 0.005 2.00e-02 2.50e+03 pdb=" N3 C B -8 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C B -8 " -0.005 2.00e-02 2.50e+03 pdb=" N4 C B -8 " -0.007 2.00e-02 2.50e+03 pdb=" C5 C B -8 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C B -8 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 112 " -0.022 2.00e-02 2.50e+03 1.08e-02 3.19e+00 pdb=" N9 A B 112 " 0.027 2.00e-02 2.50e+03 pdb=" C8 A B 112 " 0.000 2.00e-02 2.50e+03 pdb=" N7 A B 112 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A B 112 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A B 112 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A B 112 " -0.004 2.00e-02 2.50e+03 pdb=" N1 A B 112 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A B 112 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A B 112 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A B 112 " 0.002 2.00e-02 2.50e+03 ... (remaining 773 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 66 2.59 - 3.17: 5661 3.17 - 3.75: 15108 3.75 - 4.32: 21418 4.32 - 4.90: 28200 Nonbonded interactions: 70453 Sorted by model distance: nonbonded pdb=" OD1 ASP A 61 " pdb="MG MG A 502 " model vdw 2.014 2.170 nonbonded pdb=" O2' A B 69 " pdb=" O4' A B 70 " model vdw 2.139 3.040 nonbonded pdb=" OP1 U B 190 " pdb=" OH TYR A 47 " model vdw 2.204 3.040 nonbonded pdb=" O2' C B 82 " pdb=" O ASN A 155 " model vdw 2.222 3.040 nonbonded pdb=" O2' G B 76 " pdb=" O5' A B 77 " model vdw 2.230 3.040 ... (remaining 70448 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 8.620 Find NCS groups from input model: 0.020 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:6.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 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 0.105 8449 Z= 0.278 Angle : 0.710 26.798 12445 Z= 0.452 Chirality : 0.035 0.280 1529 Planarity : 0.005 0.038 776 Dihedral : 14.782 168.253 3846 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.35 (0.42), residues: 391 helix: 1.08 (0.50), residues: 120 sheet: 0.76 (0.61), residues: 72 loop : -0.45 (0.41), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 38 TYR 0.017 0.002 TYR A 6 PHE 0.009 0.001 PHE A 315 TRP 0.003 0.001 TRP A 479 HIS 0.006 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.28 ( 8449) covalent geometry : angle 0.70990 / 0.45 (12445) hydrogen bonds : bond 0.11751 / 7.24 ( 340) hydrogen bonds : angle 5.04033 / 2.86 ( 763) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.187 Fit side-chains REVERT: A 77 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7117 (tp30) REVERT: A 100 GLN cc_start: 0.8038 (tt0) cc_final: 0.7788 (tt0) REVERT: A 119 LYS cc_start: 0.8401 (mttt) cc_final: 0.8182 (mtmt) REVERT: A 168 ASN cc_start: 0.8526 (m-40) cc_final: 0.8007 (t0) REVERT: A 341 TYR cc_start: 0.7728 (p90) cc_final: 0.7521 (p90) REVERT: A 466 GLN cc_start: 0.7799 (mt0) cc_final: 0.7595 (tp40) REVERT: A 481 ARG cc_start: 0.7737 (mtt90) cc_final: 0.7510 (mtt90) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.6542 time to fit residues: 50.7956 Evaluate side-chains 50 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN A 168 ASN A 169 HIS A 195 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.174390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.118585 restraints weight = 5524.082| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 0.73 r_work: 0.3061 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8449 Z= 0.231 Angle : 0.644 7.150 12445 Z= 0.357 Chirality : 0.041 0.205 1529 Planarity : 0.006 0.045 776 Dihedral : 15.205 172.795 3039 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.75 % Allowed : 9.65 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.41 (0.41), residues: 391 helix: 1.30 (0.49), residues: 120 sheet: 0.56 (0.61), residues: 72 loop : -0.43 (0.41), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 38 TYR 0.019 0.002 TYR A 6 PHE 0.009 0.002 PHE A 315 TRP 0.003 0.002 TRP A 162 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.23 ( 8449) covalent geometry : angle 0.64445 / 0.36 (12445) hydrogen bonds : bond 0.05317 / 3.12 ( 340) hydrogen bonds : angle 3.79236 / 2.28 ( 763) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.165 Fit side-chains REVERT: A 77 GLU cc_start: 0.7680 (mt-10) cc_final: 0.6987 (tp30) REVERT: A 96 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8266 (ttpt) REVERT: A 119 LYS cc_start: 0.8352 (mttt) cc_final: 0.7946 (mtmt) REVERT: A 168 ASN cc_start: 0.8491 (m110) cc_final: 0.7865 (t0) REVERT: A 301 ASN cc_start: 0.7981 (OUTLIER) cc_final: 0.7684 (m110) REVERT: A 341 TYR cc_start: 0.7745 (p90) cc_final: 0.7302 (p90) REVERT: A 466 GLN cc_start: 0.7829 (mt0) cc_final: 0.7430 (tp40) outliers start: 6 outliers final: 4 residues processed: 48 average time/residue: 0.5747 time to fit residues: 28.9728 Evaluate side-chains 49 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 321 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 53 optimal weight: 0.0040 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.176785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.124604 restraints weight = 5464.970| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 0.63 r_work: 0.3106 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8449 Z= 0.154 Angle : 0.562 6.903 12445 Z= 0.316 Chirality : 0.037 0.183 1529 Planarity : 0.005 0.045 776 Dihedral : 15.142 170.366 3039 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.05 % Allowed : 10.23 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.66 (0.42), residues: 391 helix: 1.67 (0.48), residues: 120 sheet: 0.42 (0.60), residues: 72 loop : -0.27 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 38 TYR 0.015 0.002 TYR A 6 PHE 0.006 0.001 PHE A 41 TRP 0.003 0.001 TRP A 162 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 ( 8449) covalent geometry : angle 0.56183 / 0.32 (12445) hydrogen bonds : bond 0.04315 / 2.54 ( 340) hydrogen bonds : angle 3.53679 / 2.16 ( 763) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.180 Fit side-chains REVERT: A 77 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7197 (tt0) REVERT: A 119 LYS cc_start: 0.8339 (mttt) cc_final: 0.7917 (mtmt) REVERT: A 127 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.6924 (mp0) REVERT: A 168 ASN cc_start: 0.8483 (m110) cc_final: 0.7862 (t0) REVERT: A 301 ASN cc_start: 0.8013 (OUTLIER) cc_final: 0.7713 (m110) REVERT: A 341 TYR cc_start: 0.7690 (p90) cc_final: 0.7263 (p90) REVERT: A 466 GLN cc_start: 0.7835 (mt0) cc_final: 0.7440 (tp40) outliers start: 7 outliers final: 4 residues processed: 44 average time/residue: 0.5146 time to fit residues: 23.8318 Evaluate side-chains 47 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 321 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 13 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 19 optimal weight: 9.9990 chunk 41 optimal weight: 0.0060 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.177724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.124748 restraints weight = 5553.316| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 0.67 r_work: 0.3116 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8449 Z= 0.151 Angle : 0.545 6.763 12445 Z= 0.307 Chirality : 0.036 0.177 1529 Planarity : 0.005 0.044 776 Dihedral : 15.094 169.427 3039 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.22 % Allowed : 9.94 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.80 (0.42), residues: 391 helix: 1.97 (0.48), residues: 120 sheet: 0.27 (0.59), residues: 72 loop : -0.21 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 414 TYR 0.014 0.002 TYR A 6 PHE 0.005 0.001 PHE A 371 TRP 0.003 0.001 TRP A 162 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 ( 8449) covalent geometry : angle 0.54527 / 0.31 (12445) hydrogen bonds : bond 0.04069 / 2.38 ( 340) hydrogen bonds : angle 3.38722 / 2.09 ( 763) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.116 Fit side-chains REVERT: A 30 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7534 (mt-10) REVERT: A 77 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7214 (tt0) REVERT: A 119 LYS cc_start: 0.8328 (mttt) cc_final: 0.7911 (mtmt) REVERT: A 127 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: A 168 ASN cc_start: 0.8534 (m110) cc_final: 0.7883 (t0) REVERT: A 301 ASN cc_start: 0.8059 (OUTLIER) cc_final: 0.7775 (m110) REVERT: A 341 TYR cc_start: 0.7695 (p90) cc_final: 0.7268 (p90) REVERT: A 466 GLN cc_start: 0.7757 (mt0) cc_final: 0.7380 (tp40) REVERT: A 484 GLN cc_start: 0.8575 (tp-100) cc_final: 0.8272 (tp40) outliers start: 11 outliers final: 6 residues processed: 48 average time/residue: 0.5827 time to fit residues: 29.3029 Evaluate side-chains 48 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 321 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 0.0470 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.174635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.118983 restraints weight = 5510.138| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 0.70 r_work: 0.3069 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8449 Z= 0.205 Angle : 0.597 7.131 12445 Z= 0.332 Chirality : 0.039 0.196 1529 Planarity : 0.005 0.045 776 Dihedral : 15.148 169.738 3039 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.63 % Allowed : 11.40 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.76 (0.42), residues: 391 helix: 1.88 (0.48), residues: 120 sheet: 0.30 (0.59), residues: 72 loop : -0.22 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 414 TYR 0.016 0.002 TYR A 6 PHE 0.006 0.001 PHE A 315 TRP 0.003 0.001 TRP A 162 HIS 0.003 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.21 ( 8449) covalent geometry : angle 0.59694 / 0.33 (12445) hydrogen bonds : bond 0.04696 / 2.73 ( 340) hydrogen bonds : angle 3.51070 / 2.16 ( 763) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.174 Fit side-chains REVERT: A 77 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7271 (tt0) REVERT: A 119 LYS cc_start: 0.8364 (mttt) cc_final: 0.7943 (mtmt) REVERT: A 168 ASN cc_start: 0.8549 (m110) cc_final: 0.7871 (t0) REVERT: A 301 ASN cc_start: 0.8174 (OUTLIER) cc_final: 0.7844 (m110) REVERT: A 341 TYR cc_start: 0.7716 (p90) cc_final: 0.7246 (p90) REVERT: A 466 GLN cc_start: 0.7812 (mt0) cc_final: 0.7401 (tp40) REVERT: A 484 GLN cc_start: 0.8565 (tp-100) cc_final: 0.8264 (tp40) outliers start: 9 outliers final: 6 residues processed: 48 average time/residue: 0.5802 time to fit residues: 29.2793 Evaluate side-chains 47 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 321 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 43 optimal weight: 3.9990 chunk 39 optimal weight: 0.0030 chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.175870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.120442 restraints weight = 5539.972| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 0.78 r_work: 0.3103 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8449 Z= 0.151 Angle : 0.563 7.016 12445 Z= 0.317 Chirality : 0.036 0.185 1529 Planarity : 0.005 0.045 776 Dihedral : 15.137 168.950 3039 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.34 % Allowed : 12.28 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.85 (0.42), residues: 391 helix: 2.09 (0.49), residues: 120 sheet: 0.22 (0.59), residues: 72 loop : -0.21 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 414 TYR 0.014 0.002 TYR A 6 PHE 0.005 0.001 PHE A 315 TRP 0.004 0.001 TRP A 162 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 ( 8449) covalent geometry : angle 0.56336 / 0.32 (12445) hydrogen bonds : bond 0.04260 / 2.48 ( 340) hydrogen bonds : angle 3.45494 / 2.14 ( 763) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.177 Fit side-chains REVERT: A 30 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7172 (mt-10) REVERT: A 77 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7265 (tt0) REVERT: A 96 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8264 (ttpt) REVERT: A 119 LYS cc_start: 0.8332 (mttt) cc_final: 0.7910 (mtmt) REVERT: A 126 GLU cc_start: 0.7513 (mm-30) cc_final: 0.6848 (mp0) REVERT: A 168 ASN cc_start: 0.8564 (m110) cc_final: 0.7882 (t0) REVERT: A 301 ASN cc_start: 0.8076 (OUTLIER) cc_final: 0.7770 (m110) REVERT: A 341 TYR cc_start: 0.7712 (p90) cc_final: 0.7292 (p90) REVERT: A 466 GLN cc_start: 0.7779 (mt0) cc_final: 0.7380 (tp40) outliers start: 8 outliers final: 6 residues processed: 45 average time/residue: 0.6346 time to fit residues: 30.0027 Evaluate side-chains 48 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 321 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.171498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.115224 restraints weight = 5537.832| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 0.82 r_work: 0.3025 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 8449 Z= 0.337 Angle : 0.729 7.992 12445 Z= 0.393 Chirality : 0.046 0.219 1529 Planarity : 0.007 0.044 776 Dihedral : 15.316 171.805 3039 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.22 % Allowed : 11.40 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.58 (0.41), residues: 391 helix: 1.64 (0.48), residues: 120 sheet: 0.27 (0.60), residues: 72 loop : -0.29 (0.41), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 106 TYR 0.021 0.003 TYR A 6 PHE 0.009 0.002 PHE A 315 TRP 0.004 0.002 TRP A 479 HIS 0.005 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00687 / 0.34 ( 8449) covalent geometry : angle 0.72895 / 0.39 (12445) hydrogen bonds : bond 0.05942 / 3.44 ( 340) hydrogen bonds : angle 3.72813 / 2.31 ( 763) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.193 Fit side-chains REVERT: A 30 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7213 (mt-10) REVERT: A 77 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7308 (tt0) REVERT: A 96 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8274 (ttpt) REVERT: A 119 LYS cc_start: 0.8420 (mttt) cc_final: 0.7988 (mtmt) REVERT: A 301 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.7911 (m110) REVERT: A 341 TYR cc_start: 0.7770 (p90) cc_final: 0.7340 (p90) REVERT: A 466 GLN cc_start: 0.7763 (mt0) cc_final: 0.7387 (tp40) outliers start: 11 outliers final: 7 residues processed: 50 average time/residue: 0.6571 time to fit residues: 34.5547 Evaluate side-chains 51 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 421 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.176291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.122948 restraints weight = 5571.520| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 0.64 r_work: 0.3112 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8449 Z= 0.153 Angle : 0.564 7.166 12445 Z= 0.317 Chirality : 0.037 0.177 1529 Planarity : 0.004 0.046 776 Dihedral : 15.215 169.474 3039 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.34 % Allowed : 11.99 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.83 (0.42), residues: 391 helix: 2.00 (0.49), residues: 120 sheet: 0.17 (0.60), residues: 72 loop : -0.16 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 414 TYR 0.014 0.001 TYR A 6 PHE 0.006 0.001 PHE A 41 TRP 0.004 0.001 TRP A 162 HIS 0.003 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 ( 8449) covalent geometry : angle 0.56353 / 0.32 (12445) hydrogen bonds : bond 0.04282 / 2.51 ( 340) hydrogen bonds : angle 3.49756 / 2.18 ( 763) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.198 Fit side-chains REVERT: A 77 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7250 (tt0) REVERT: A 119 LYS cc_start: 0.8346 (mttt) cc_final: 0.7935 (mtmt) REVERT: A 126 GLU cc_start: 0.7567 (mm-30) cc_final: 0.6945 (mp0) REVERT: A 168 ASN cc_start: 0.8591 (m110) cc_final: 0.7926 (t0) REVERT: A 301 ASN cc_start: 0.8162 (OUTLIER) cc_final: 0.7838 (m110) REVERT: A 341 TYR cc_start: 0.7716 (p90) cc_final: 0.7313 (p90) REVERT: A 466 GLN cc_start: 0.7776 (mt0) cc_final: 0.7399 (tp40) outliers start: 8 outliers final: 7 residues processed: 47 average time/residue: 0.6318 time to fit residues: 31.3477 Evaluate side-chains 50 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 360 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 36 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.176773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.124650 restraints weight = 5496.830| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 0.58 r_work: 0.3115 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8449 Z= 0.141 Angle : 0.549 6.849 12445 Z= 0.309 Chirality : 0.036 0.180 1529 Planarity : 0.004 0.046 776 Dihedral : 15.125 169.514 3039 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.92 % Allowed : 12.28 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.93 (0.42), residues: 391 helix: 2.10 (0.48), residues: 120 sheet: 0.24 (0.60), residues: 71 loop : -0.09 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 414 TYR 0.014 0.002 TYR A 6 PHE 0.005 0.001 PHE A 315 TRP 0.003 0.001 TRP A 162 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.14 ( 8449) covalent geometry : angle 0.54940 / 0.31 (12445) hydrogen bonds : bond 0.04113 / 2.40 ( 340) hydrogen bonds : angle 3.37896 / 2.10 ( 763) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.231 Fit side-chains REVERT: A 77 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7270 (tt0) REVERT: A 119 LYS cc_start: 0.8339 (mttt) cc_final: 0.7925 (mtmt) REVERT: A 126 GLU cc_start: 0.7540 (mm-30) cc_final: 0.6937 (mp0) REVERT: A 168 ASN cc_start: 0.8578 (m110) cc_final: 0.7888 (t0) REVERT: A 301 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7819 (m110) REVERT: A 341 TYR cc_start: 0.7638 (p90) cc_final: 0.7230 (p90) REVERT: A 466 GLN cc_start: 0.7747 (mt0) cc_final: 0.7385 (tp40) outliers start: 10 outliers final: 7 residues processed: 48 average time/residue: 0.5971 time to fit residues: 30.2382 Evaluate side-chains 50 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 360 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.176818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.124120 restraints weight = 5541.894| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 0.81 r_work: 0.3106 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8449 Z= 0.145 Angle : 0.548 6.882 12445 Z= 0.308 Chirality : 0.036 0.177 1529 Planarity : 0.004 0.046 776 Dihedral : 15.124 169.512 3039 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.05 % Allowed : 13.16 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.93 (0.42), residues: 391 helix: 2.11 (0.48), residues: 120 sheet: 0.22 (0.60), residues: 71 loop : -0.10 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 414 TYR 0.014 0.002 TYR A 6 PHE 0.005 0.001 PHE A 315 TRP 0.003 0.001 TRP A 162 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.15 ( 8449) covalent geometry : angle 0.54807 / 0.31 (12445) hydrogen bonds : bond 0.04068 / 2.38 ( 340) hydrogen bonds : angle 3.37441 / 2.10 ( 763) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 782 Ramachandran restraints generated. 391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.184 Fit side-chains REVERT: A 77 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7088 (tt0) REVERT: A 119 LYS cc_start: 0.8265 (mttt) cc_final: 0.7790 (mtmt) REVERT: A 126 GLU cc_start: 0.7492 (mm-30) cc_final: 0.6805 (mp0) REVERT: A 168 ASN cc_start: 0.8585 (m110) cc_final: 0.7795 (t0) REVERT: A 301 ASN cc_start: 0.7975 (OUTLIER) cc_final: 0.7680 (m110) REVERT: A 341 TYR cc_start: 0.7550 (p90) cc_final: 0.7108 (p90) REVERT: A 466 GLN cc_start: 0.7664 (mt0) cc_final: 0.7212 (tp40) outliers start: 7 outliers final: 6 residues processed: 46 average time/residue: 0.6230 time to fit residues: 30.1222 Evaluate side-chains 49 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 321 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 2 optimal weight: 5.9990 chunk 29 optimal weight: 0.4980 chunk 19 optimal weight: 10.0000 chunk 36 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 46 optimal weight: 0.0770 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.177226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.124933 restraints weight = 5555.958| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 0.62 r_work: 0.3125 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 8449 Z= 0.123 Angle : 0.538 6.773 12445 Z= 0.304 Chirality : 0.035 0.176 1529 Planarity : 0.004 0.046 776 Dihedral : 15.120 169.030 3039 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.05 % Allowed : 13.16 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.93 (0.42), residues: 391 helix: 2.13 (0.48), residues: 120 sheet: 0.21 (0.60), residues: 71 loop : -0.10 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 414 TYR 0.014 0.001 TYR A 6 PHE 0.005 0.001 PHE A 454 TRP 0.003 0.001 TRP A 162 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.12 ( 8449) covalent geometry : angle 0.53777 / 0.30 (12445) hydrogen bonds : bond 0.04005 / 2.34 ( 340) hydrogen bonds : angle 3.36692 / 2.09 ( 763) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2755.42 seconds wall clock time: 47 minutes 33.69 seconds (2853.69 seconds total)