Starting phenix.real_space_refine on Fri Sep 11 05:41:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xht_33198/09_2026/7xht_33198.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xht_33198/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7xht_33198/09_2026/7xht_33198.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xht_33198/09_2026/7xht_33198.cif" model { file = "/net/cci-nas-00/data/ceres_data/7xht_33198/09_2026/7xht_33198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xht_33198/09_2026/7xht_33198.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xht_33198/09_2026/7xht_33198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xht_33198/09_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-2.2.1-6174/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: {'RNAv2': 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: 1.40, per 1000 atoms: 0.18 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: 0.82 Conformation dependent library (CDL) restraints added in 139.6 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: 1.02 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: 1.60 Time building geometry restraints manager: 1.05 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: 12427 5.36 - 10.72: 14 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=" C3' DT C 11 " pdb=" O3' DT C 11 " pdb=" P DA C 12 " ideal model delta sigma weight residual 119.70 110.80 8.90 1.20e+00 6.94e-01 5.50e+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=" 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 1.90e+00 2.77e-01 3.97e+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 1.90e+00 2.77e-01 2.39e+01 ... (remaining 12440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.65: 4122 33.65 - 67.30: 436 67.30 - 100.95: 27 100.95 - 134.60: 0 134.60 - 168.25: 1 Dihedral angle restraints: 4586 sinusoidal: 3437 harmonic: 1149 Sorted by residual: dihedral pdb=" C4' A B 68 " pdb=" C3' A B 68 " pdb=" C2' A B 68 " pdb=" C1' A B 68 " ideal model delta sinusoidal sigma weight residual 36.34 -38.62 74.96 1 3.10e+00 1.04e-01 7.40e+02 dihedral pdb=" C4' U B 187 " pdb=" C3' U B 187 " pdb=" C2' U B 187 " pdb=" C1' U B 187 " ideal model delta sinusoidal sigma weight residual 36.34 -38.45 74.80 1 3.10e+00 1.04e-01 7.37e+02 dihedral pdb=" C4' A B 149 " pdb=" C3' A B 149 " pdb=" C2' A B 149 " pdb=" C1' A B 149 " ideal model delta sinusoidal sigma weight residual 36.35 -37.36 73.71 1 3.10e+00 1.04e-01 7.19e+02 ... (remaining 4583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1185 0.068 - 0.135: 109 0.135 - 0.203: 15 0.203 - 0.270: 188 0.270 - 0.338: 32 Chirality restraints: 1529 Sorted by residual: chirality pdb=" P A B 77 " pdb=" OP1 A B 77 " pdb=" OP2 A B 77 " pdb=" O5' A B 77 " both_signs ideal model delta sigma weight residual True 2.17 -2.51 -0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" C2' A B 68 " pdb=" C3' A B 68 " pdb=" O2' A B 68 " pdb=" C1' A B 68 " both_signs ideal model delta sigma weight residual False -2.79 -2.47 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C2' U B 187 " pdb=" C3' U B 187 " pdb=" O2' U B 187 " pdb=" C1' U B 187 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.47e+00 ... (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: 3.490 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.740 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:7.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.120 ------------------------------------------------------------------------------- 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= 0.291 Angle : 0.958 26.798 12445 Z= 0.500 Chirality : 0.099 0.338 1529 Planarity : 0.005 0.038 776 Dihedral : 19.858 168.253 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 0.00427 / 0.29 ( 8449) covalent geometry : angle 0.95792 / 0.50 (12445) hydrogen bonds : bond 0.11751 / 6.10 ( 340) hydrogen bonds : angle 5.04033 / 1.97 ( 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: 0.6616 time to fit residues: 51.1799 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 : 0.143 ------------------------------------------------------------------------------- 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: 4.9990 chunk 16 optimal weight: 9.9990 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 = 0.3921 r_free = 0.3921 target = 0.177672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.123334 restraints weight = 5553.269| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 0.73 r_work: 0.3135 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8449 Z= 0.304 Angle : 1.480 27.143 12445 Z= 0.604 Chirality : 0.145 1.517 1529 Planarity : 0.006 0.045 776 Dihedral : 18.537 172.838 3039 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.46 % Allowed : 9.65 % Favored : 88.89 % 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: 1.26 (0.49), residues: 120 sheet: 0.59 (0.61), residues: 72 loop : -0.43 (0.41), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 38 TYR 0.019 0.002 TYR A 6 PHE 0.008 0.002 PHE A 315 TRP 0.003 0.001 TRP A 479 HIS 0.004 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.30 ( 8449) covalent geometry : angle 1.48032 / 0.60 (12445) hydrogen bonds : bond 0.05534 / 2.91 ( 340) hydrogen bonds : angle 3.83761 / 1.54 ( 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 50 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.112 Fit side-chains REVERT: A 77 GLU cc_start: 0.7664 (mt-10) cc_final: 0.6989 (tp30) REVERT: A 96 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8271 (ttpt) REVERT: A 119 LYS cc_start: 0.8340 (mttt) cc_final: 0.7938 (mtmt) REVERT: A 168 ASN cc_start: 0.8506 (m110) cc_final: 0.7858 (t0) REVERT: A 301 ASN cc_start: 0.7983 (OUTLIER) cc_final: 0.7702 (m110) REVERT: A 341 TYR cc_start: 0.7733 (p90) cc_final: 0.7296 (p90) REVERT: A 466 GLN cc_start: 0.7779 (mt0) cc_final: 0.7393 (tp40) outliers start: 5 outliers final: 4 residues processed: 47 average time/residue: 0.6130 time to fit residues: 30.3032 Evaluate side-chains 50 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.155 ------------------------------------------------------------------------------- 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 301 ASN Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 411 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 16 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.187625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.152882 restraints weight = 5400.200| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 0.87 r_work: 0.3124 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8449 Z= 0.222 Angle : 1.135 19.684 12445 Z= 0.476 Chirality : 0.104 0.981 1529 Planarity : 0.005 0.047 776 Dihedral : 18.921 169.526 3039 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.05 % Allowed : 10.53 % Favored : 87.43 % 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: 0.61 (0.42), residues: 391 helix: 1.57 (0.48), residues: 120 sheet: 0.43 (0.60), residues: 72 loop : -0.28 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 38 TYR 0.017 0.002 TYR A 6 PHE 0.007 0.001 PHE A 41 TRP 0.003 0.001 TRP A 162 HIS 0.003 0.001 HIS A 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.22 ( 8449) covalent geometry : angle 1.13524 / 0.48 (12445) hydrogen bonds : bond 0.05125 / 2.63 ( 340) hydrogen bonds : angle 3.60399 / 1.45 ( 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 47 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.156 Fit side-chains REVERT: A 77 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7555 (tp30) REVERT: A 119 LYS cc_start: 0.8484 (mttt) cc_final: 0.8130 (mtmt) REVERT: A 127 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: A 168 ASN cc_start: 0.8655 (m110) cc_final: 0.8037 (t0) REVERT: A 301 ASN cc_start: 0.8401 (OUTLIER) cc_final: 0.8155 (m110) REVERT: A 341 TYR cc_start: 0.7938 (p90) cc_final: 0.7601 (p90) REVERT: A 466 GLN cc_start: 0.8208 (mt0) cc_final: 0.7853 (tp40) outliers start: 7 outliers final: 4 residues processed: 44 average time/residue: 0.6305 time to fit residues: 29.2393 Evaluate side-chains 45 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 13 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.186252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.152491 restraints weight = 5491.057| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 0.82 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8449 Z= 0.227 Angle : 1.056 13.222 12445 Z= 0.449 Chirality : 0.092 0.840 1529 Planarity : 0.005 0.048 776 Dihedral : 19.274 171.140 3039 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.92 % Allowed : 10.53 % Favored : 86.55 % 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 (0.41), residues: 391 helix: 1.73 (0.48), residues: 120 sheet: 0.29 (0.59), residues: 72 loop : -0.25 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 147 TYR 0.017 0.002 TYR A 6 PHE 0.007 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 0.00455 / 0.23 ( 8449) covalent geometry : angle 1.05592 / 0.45 (12445) hydrogen bonds : bond 0.05055 / 2.58 ( 340) hydrogen bonds : angle 3.57369 / 1.44 ( 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 52 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.188 Fit side-chains REVERT: A 96 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8037 (ttpt) REVERT: A 168 ASN cc_start: 0.8207 (m110) cc_final: 0.7786 (t0) REVERT: A 301 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.7932 (m110) outliers start: 10 outliers final: 7 residues processed: 48 average time/residue: 0.7443 time to fit residues: 37.4850 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 : 0.187 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 360 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 5.9990 chunk 44 optimal weight: 0.0970 chunk 54 optimal weight: 0.0470 chunk 42 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.191457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.155966 restraints weight = 5485.108| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 0.91 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8449 Z= 0.160 Angle : 0.944 11.706 12445 Z= 0.405 Chirality : 0.081 0.680 1529 Planarity : 0.004 0.046 776 Dihedral : 19.231 167.396 3039 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.63 % Allowed : 12.87 % Favored : 84.50 % 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: 0.84 (0.42), residues: 391 helix: 1.93 (0.48), residues: 120 sheet: 0.28 (0.59), residues: 71 loop : -0.13 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 414 TYR 0.021 0.002 TYR A 341 PHE 0.006 0.001 PHE A 41 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 0.00300 / 0.16 ( 8449) covalent geometry : angle 0.94380 / 0.40 (12445) hydrogen bonds : bond 0.04380 / 2.22 ( 340) hydrogen bonds : angle 3.34625 / 1.36 ( 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 : 0.187 Fit side-chains REVERT: A 168 ASN cc_start: 0.8295 (m110) cc_final: 0.7848 (t0) outliers start: 9 outliers final: 6 residues processed: 47 average time/residue: 0.7415 time to fit residues: 36.4559 Evaluate side-chains 46 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 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 189 LYS 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: 6.9990 chunk 39 optimal weight: 0.0270 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 overall best weight: 1.2642 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.186066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.155021 restraints weight = 5538.132| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 0.43 r_work: 0.3283 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8449 Z= 0.205 Angle : 0.987 12.590 12445 Z= 0.422 Chirality : 0.084 0.754 1529 Planarity : 0.005 0.047 776 Dihedral : 19.213 168.998 3039 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.92 % Allowed : 12.87 % Favored : 84.21 % 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: 0.87 (0.42), residues: 391 helix: 1.95 (0.48), residues: 120 sheet: 0.30 (0.60), residues: 71 loop : -0.11 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 414 TYR 0.022 0.002 TYR A 341 PHE 0.006 0.001 PHE A 41 TRP 0.003 0.001 TRP A 162 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.20 ( 8449) covalent geometry : angle 0.98709 / 0.42 (12445) hydrogen bonds : bond 0.04728 / 2.40 ( 340) hydrogen bonds : angle 3.45251 / 1.40 ( 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 51 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.213 Fit side-chains REVERT: A 52 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6531 (mp0) REVERT: A 168 ASN cc_start: 0.8540 (m110) cc_final: 0.7940 (t0) REVERT: A 301 ASN cc_start: 0.8336 (OUTLIER) cc_final: 0.8082 (m110) outliers start: 10 outliers final: 7 residues processed: 46 average time/residue: 0.8154 time to fit residues: 39.2469 Evaluate side-chains 49 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 52 GLU 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 Chi-restraints excluded: chain A residue 360 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 = 0.176264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.123772 restraints weight = 5561.129| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 0.63 r_work: 0.3090 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 8449 Z= 0.302 Angle : 1.129 15.087 12445 Z= 0.480 Chirality : 0.094 0.888 1529 Planarity : 0.006 0.046 776 Dihedral : 19.371 172.121 3039 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.51 % Allowed : 11.99 % Favored : 84.50 % 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: 0.73 (0.42), residues: 391 helix: 1.76 (0.48), residues: 120 sheet: 0.36 (0.60), residues: 71 loop : -0.21 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 152 TYR 0.023 0.003 TYR A 341 PHE 0.009 0.002 PHE A 315 TRP 0.004 0.002 TRP A 479 HIS 0.004 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.30 ( 8449) covalent geometry : angle 1.12934 / 0.48 (12445) hydrogen bonds : bond 0.05760 / 2.95 ( 340) hydrogen bonds : angle 3.70889 / 1.50 ( 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: 12 poor density : 42 time to evaluate : 0.190 Fit side-chains REVERT: A 301 ASN cc_start: 0.8285 (OUTLIER) cc_final: 0.7943 (m110) outliers start: 12 outliers final: 7 residues processed: 49 average time/residue: 0.7359 time to fit residues: 37.8209 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 : 0.189 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 54 optimal weight: 0.2980 chunk 3 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN A 484 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.178494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.127340 restraints weight = 5578.959| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 0.64 r_work: 0.3118 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8449 Z= 0.220 Angle : 1.033 13.421 12445 Z= 0.442 Chirality : 0.088 0.807 1529 Planarity : 0.005 0.046 776 Dihedral : 19.329 169.844 3039 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.34 % Allowed : 14.04 % Favored : 83.63 % 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: 1.81 (0.48), residues: 120 sheet: 0.30 (0.61), residues: 71 loop : -0.17 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 414 TYR 0.025 0.002 TYR A 341 PHE 0.007 0.001 PHE A 315 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 0.00441 / 0.22 ( 8449) covalent geometry : angle 1.03343 / 0.44 (12445) hydrogen bonds : bond 0.05052 / 2.57 ( 340) hydrogen bonds : angle 3.60018 / 1.46 ( 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 : 0.195 Fit side-chains REVERT: A 301 ASN cc_start: 0.8200 (OUTLIER) cc_final: 0.7879 (m110) outliers start: 8 outliers final: 6 residues processed: 46 average time/residue: 0.7080 time to fit residues: 34.2264 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 : 0.185 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN A 484 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.180028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.128801 restraints weight = 5520.856| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 0.64 r_work: 0.3157 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8449 Z= 0.178 Angle : 0.993 12.570 12445 Z= 0.425 Chirality : 0.084 0.779 1529 Planarity : 0.005 0.046 776 Dihedral : 19.319 168.444 3039 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.63 % Allowed : 14.04 % Favored : 83.33 % 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: 0.87 (0.42), residues: 391 helix: 2.00 (0.49), residues: 120 sheet: 0.26 (0.61), residues: 71 loop : -0.12 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 102 TYR 0.027 0.002 TYR A 341 PHE 0.005 0.001 PHE A 371 TRP 0.005 0.001 TRP A 162 HIS 0.003 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.18 ( 8449) covalent geometry : angle 0.99332 / 0.43 (12445) hydrogen bonds : bond 0.04682 / 2.37 ( 340) hydrogen bonds : angle 3.55662 / 1.45 ( 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 50 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.186 Fit side-chains REVERT: A 301 ASN cc_start: 0.8155 (OUTLIER) cc_final: 0.7837 (m110) outliers start: 9 outliers final: 6 residues processed: 46 average time/residue: 0.7353 time to fit residues: 35.5495 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 : 0.184 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 40 optimal weight: 0.0010 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN A 484 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.182046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.131615 restraints weight = 5571.114| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 0.58 r_work: 0.3205 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8449 Z= 0.171 Angle : 0.966 11.523 12445 Z= 0.415 Chirality : 0.083 0.741 1529 Planarity : 0.004 0.047 776 Dihedral : 19.272 168.068 3039 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.34 % Allowed : 14.62 % Favored : 83.04 % 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: 0.92 (0.42), residues: 391 helix: 2.03 (0.48), residues: 120 sheet: 0.21 (0.60), residues: 71 loop : -0.05 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 414 TYR 0.026 0.002 TYR A 341 PHE 0.006 0.001 PHE A 41 TRP 0.006 0.001 TRP A 162 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.17 ( 8449) covalent geometry : angle 0.96631 / 0.41 (12445) hydrogen bonds : bond 0.04575 / 2.32 ( 340) hydrogen bonds : angle 3.43762 / 1.40 ( 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 50 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.190 Fit side-chains REVERT: A 301 ASN cc_start: 0.8105 (OUTLIER) cc_final: 0.7808 (m110) outliers start: 8 outliers final: 6 residues processed: 46 average time/residue: 0.7039 time to fit residues: 34.0719 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 : 0.177 ------------------------------------------------------------------------------- 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 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 2 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 chunk 36 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN A 484 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.177795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.128671 restraints weight = 5577.057| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 0.54 r_work: 0.3170 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2014 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= 0.260 Angle : 1.055 13.838 12445 Z= 0.450 Chirality : 0.088 0.848 1529 Planarity : 0.005 0.047 776 Dihedral : 19.278 170.656 3039 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.92 % Allowed : 14.04 % Favored : 83.04 % 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: 0.86 (0.42), residues: 391 helix: 1.96 (0.48), residues: 120 sheet: 0.33 (0.61), residues: 71 loop : -0.14 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 152 TYR 0.027 0.003 TYR A 341 PHE 0.008 0.002 PHE A 315 TRP 0.003 0.001 TRP A 479 HIS 0.003 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.26 ( 8449) covalent geometry : angle 1.05509 / 0.45 (12445) hydrogen bonds : bond 0.05213 / 2.66 ( 340) hydrogen bonds : angle 3.57594 / 1.45 ( 763) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2718.36 seconds wall clock time: 47 minutes 9.18 seconds (2829.18 seconds total)