Starting phenix.real_space_refine on Thu Jul 2 10:02:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ctl_26994/07_2026/8ctl_26994_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ctl_26994/07_2026/8ctl_26994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ctl_26994/07_2026/8ctl_26994_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ctl_26994/07_2026/8ctl_26994_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ctl_26994/07_2026/8ctl_26994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ctl_26994/07_2026/8ctl_26994.map" } resolution = 3.1 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 233 5.49 5 S 21 5.16 5 C 4257 2.51 5 N 1486 2.21 5 O 2141 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 8138 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 3209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3209 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 382} Chain breaks: 1 Chain: "C" Number of atoms: 3937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 3937 Classifications: {'RNA': 184} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 11, 'rna3p_pur': 89, 'rna3p_pyr': 69} Link IDs: {'rna2p': 26, 'rna3p': 157} Chain breaks: 2 Chain: "A" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 579 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "B" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 413 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Time building chain proxies: 1.34, per 1000 atoms: 0.16 Number of scatterers: 8138 At special positions: 0 Unit cell: (89.88, 103.79, 131.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 P 233 15.00 O 2141 8.00 N 1486 7.00 C 4257 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: 0.49 Conformation dependent library (CDL) restraints added in 180.9 milliseconds 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 752 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 6 sheets defined 29.9% alpha, 18.2% beta 75 base pairs and 130 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'D' and resid 20 through 29 removed outlier: 3.755A pdb=" N LEU D 27 " --> pdb=" O VAL D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 108 Processing helix chain 'D' and resid 109 through 121 Processing helix chain 'D' and resid 163 through 181 Processing helix chain 'D' and resid 297 through 313 Proline residue: D 304 - end of helix Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 338 through 340 No H-bonds generated for 'chain 'D' and resid 338 through 340' Processing helix chain 'D' and resid 341 through 349 removed outlier: 3.658A pdb=" N CYS D 345 " --> pdb=" O LEU D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 416 Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 480 through 482 No H-bonds generated for 'chain 'D' and resid 480 through 482' Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 14 removed outlier: 4.626A pdb=" N VAL D 6 " --> pdb=" O LEU D 14 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TYR D 5 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU D 44 " --> pdb=" O TYR D 5 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE D 7 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N THR D 41 " --> pdb=" O VAL D 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 318 through 322 removed outlier: 6.256A pdb=" N VAL D 189 " --> pdb=" O CYS D 319 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THR D 321 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU D 191 " --> pdb=" O THR D 321 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET D 68 " --> pdb=" O ALA D 81 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N THR D 72 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N SER D 77 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL D 367 " --> pdb=" O GLN D 82 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N MET D 366 " --> pdb=" O TYR D 494 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 128 through 131 Processing sheet with id=AA4, first strand: chain 'D' and resid 378 through 380 Processing sheet with id=AA5, first strand: chain 'D' and resid 387 through 388 removed outlier: 6.045A pdb=" N TYR D 387 " --> pdb=" O VAL D 394 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 476 through 478 removed outlier: 6.535A pdb=" N TYR D 468 " --> pdb=" O SER D 458 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N SER D 458 " --> pdb=" O TYR D 468 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL D 470 " --> pdb=" O SER D 456 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL D 446 " --> pdb=" O TYR D 484 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N TYR D 484 " --> pdb=" O VAL D 446 " (cutoff:3.500A) 114 hydrogen bonds defined for protein. 324 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 190 hydrogen bonds 356 hydrogen bond angles 0 basepair planarities 75 basepair parallelities 130 stacking parallelities Total time for adding SS restraints: 1.33 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 785 1.30 - 1.43: 3479 1.43 - 1.56: 4025 1.56 - 1.69: 460 1.69 - 1.81: 33 Bond restraints: 8782 Sorted by residual: bond pdb=" CA ARG D 131 " pdb=" C ARG D 131 " ideal model delta sigma weight residual 1.526 1.456 0.070 1.20e-02 6.94e+03 3.38e+01 bond pdb=" CA ALA D 381 " pdb=" C ALA D 381 " ideal model delta sigma weight residual 1.526 1.452 0.074 1.30e-02 5.92e+03 3.20e+01 bond pdb=" CA ARG D 371 " pdb=" C ARG D 371 " ideal model delta sigma weight residual 1.525 1.460 0.065 1.28e-02 6.10e+03 2.55e+01 bond pdb=" N GLN D 465 " pdb=" CA GLN D 465 " ideal model delta sigma weight residual 1.461 1.402 0.059 1.20e-02 6.94e+03 2.46e+01 bond pdb=" C ARG D 131 " pdb=" O ARG D 131 " ideal model delta sigma weight residual 1.235 1.178 0.056 1.14e-02 7.69e+03 2.45e+01 ... (remaining 8777 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 11671 2.17 - 4.35: 1139 4.35 - 6.52: 115 6.52 - 8.70: 18 8.70 - 10.87: 14 Bond angle restraints: 12957 Sorted by residual: angle pdb=" N THR D 352 " pdb=" CA THR D 352 " pdb=" C THR D 352 " ideal model delta sigma weight residual 111.03 121.20 -10.17 1.11e+00 8.12e-01 8.39e+01 angle pdb=" N ARG D 398 " pdb=" CA ARG D 398 " pdb=" C ARG D 398 " ideal model delta sigma weight residual 113.41 102.54 10.87 1.22e+00 6.72e-01 7.95e+01 angle pdb=" N ILE D 439 " pdb=" CA ILE D 439 " pdb=" C ILE D 439 " ideal model delta sigma weight residual 108.93 99.38 9.55 1.35e+00 5.49e-01 5.00e+01 angle pdb=" CA GLY D 460 " pdb=" C GLY D 460 " pdb=" O GLY D 460 " ideal model delta sigma weight residual 122.22 117.63 4.59 6.50e-01 2.37e+00 4.98e+01 angle pdb=" C THR D 352 " pdb=" CA THR D 352 " pdb=" CB THR D 352 " ideal model delta sigma weight residual 110.95 100.80 10.15 1.55e+00 4.16e-01 4.29e+01 ... (remaining 12952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 4525 35.28 - 70.56: 733 70.56 - 105.84: 69 105.84 - 141.12: 11 141.12 - 176.40: 13 Dihedral angle restraints: 5351 sinusoidal: 4183 harmonic: 1168 Sorted by residual: dihedral pdb=" C5' A C 93 " pdb=" C4' A C 93 " pdb=" C3' A C 93 " pdb=" O3' A C 93 " ideal model delta sinusoidal sigma weight residual 147.00 77.07 69.93 1 8.00e+00 1.56e-02 9.85e+01 dihedral pdb=" O4' C C 60 " pdb=" C1' C C 60 " pdb=" N1 C C 60 " pdb=" C2 C C 60 " ideal model delta sinusoidal sigma weight residual 200.00 31.04 168.96 1 1.50e+01 4.44e-03 8.45e+01 dihedral pdb=" C4' A C 93 " pdb=" C3' A C 93 " pdb=" C2' A C 93 " pdb=" C1' A C 93 " ideal model delta sinusoidal sigma weight residual -35.00 27.93 -62.93 1 8.00e+00 1.56e-02 8.17e+01 ... (remaining 5348 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1099 0.093 - 0.185: 441 0.185 - 0.278: 44 0.278 - 0.370: 4 0.370 - 0.463: 4 Chirality restraints: 1592 Sorted by residual: chirality pdb=" C3' DT B 113 " pdb=" C4' DT B 113 " pdb=" O3' DT B 113 " pdb=" C2' DT B 113 " both_signs ideal model delta sigma weight residual False -2.73 -2.27 -0.46 2.00e-01 2.50e+01 5.35e+00 chirality pdb=" C3' DT B 109 " pdb=" C4' DT B 109 " pdb=" O3' DT B 109 " pdb=" C2' DT B 109 " both_signs ideal model delta sigma weight residual False -2.73 -2.28 -0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" CA LYS D 31 " pdb=" N LYS D 31 " pdb=" C LYS D 31 " pdb=" CB LYS D 31 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.13e+00 ... (remaining 1589 not shown) Planarity restraints: 798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC A 27 " 0.052 2.00e-02 2.50e+03 2.51e-02 1.42e+01 pdb=" N1 DC A 27 " -0.048 2.00e-02 2.50e+03 pdb=" C2 DC A 27 " -0.008 2.00e-02 2.50e+03 pdb=" O2 DC A 27 " -0.009 2.00e-02 2.50e+03 pdb=" N3 DC A 27 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DC A 27 " 0.012 2.00e-02 2.50e+03 pdb=" N4 DC A 27 " 0.014 2.00e-02 2.50e+03 pdb=" C5 DC A 27 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DC A 27 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A C 78 " 0.048 2.00e-02 2.50e+03 2.24e-02 1.38e+01 pdb=" N9 A C 78 " -0.053 2.00e-02 2.50e+03 pdb=" C8 A C 78 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A C 78 " 0.005 2.00e-02 2.50e+03 pdb=" C5 A C 78 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A C 78 " 0.009 2.00e-02 2.50e+03 pdb=" N6 A C 78 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A C 78 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A C 78 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A C 78 " -0.008 2.00e-02 2.50e+03 pdb=" C4 A C 78 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG A 9 " 0.038 2.00e-02 2.50e+03 1.94e-02 1.13e+01 pdb=" N9 DG A 9 " -0.051 2.00e-02 2.50e+03 pdb=" C8 DG A 9 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG A 9 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DG A 9 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DG A 9 " 0.013 2.00e-02 2.50e+03 pdb=" O6 DG A 9 " -0.003 2.00e-02 2.50e+03 pdb=" N1 DG A 9 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG A 9 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG A 9 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DG A 9 " -0.009 2.00e-02 2.50e+03 pdb=" C4 DG A 9 " -0.008 2.00e-02 2.50e+03 ... (remaining 795 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2129 2.80 - 3.33: 7862 3.33 - 3.85: 17670 3.85 - 4.38: 20559 4.38 - 4.90: 26863 Nonbonded interactions: 75083 Sorted by model distance: nonbonded pdb=" OG SER D 8 " pdb=" OG SER D 10 " model vdw 2.280 3.040 nonbonded pdb=" O2' G C 95 " pdb=" N2 G C 131 " model vdw 2.309 3.120 nonbonded pdb=" OD1 ASN D 154 " pdb=" O2' U C 125 " model vdw 2.321 3.040 nonbonded pdb=" N3 C C 111 " pdb=" O6 G C 172 " model vdw 2.327 2.496 nonbonded pdb=" O ASN D 154 " pdb=" O2' C C 98 " model vdw 2.352 3.040 ... (remaining 75078 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.310 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4578 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 : 0.009 0.074 8782 Z= 0.671 Angle : 1.308 10.875 12957 Z= 0.940 Chirality : 0.091 0.463 1592 Planarity : 0.005 0.071 798 Dihedral : 27.577 176.404 4599 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 32.18 Ramachandran Plot: Outliers : 0.50 % Allowed : 12.09 % Favored : 87.41 % Rotamer: Outliers : 7.20 % Allowed : 17.00 % Favored : 75.79 % Cbeta Deviations : 1.06 % 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: -5.68 (0.29), residues: 397 helix: -4.32 (0.23), residues: 113 sheet: -3.35 (0.52), residues: 72 loop : -3.66 (0.30), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 86 TYR 0.011 0.002 TYR D 433 PHE 0.012 0.002 PHE D 196 TRP 0.004 0.001 TRP D 161 HIS 0.008 0.002 HIS D 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00934 / 0.67 ( 8782) covalent geometry : angle 1.30800 / 0.94 (12957) hydrogen bonds : bond 0.22740 / 15.16 ( 304) hydrogen bonds : angle 14.52390 / 9.60 ( 680) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 175 ASN cc_start: 0.6017 (m-40) cc_final: 0.5698 (m-40) REVERT: D 443 SER cc_start: 0.6737 (m) cc_final: 0.6077 (t) REVERT: D 470 VAL cc_start: 0.5463 (OUTLIER) cc_final: 0.5218 (t) outliers start: 25 outliers final: 3 residues processed: 129 average time/residue: 0.1131 time to fit residues: 17.9286 Evaluate side-chains 77 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 470 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 56 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 53 GLN D 373 HIS ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 462 ASN D 465 GLN D 487 ASN ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.127463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.093107 restraints weight = 14093.114| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.83 r_work: 0.3312 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6319 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 8782 Z= 0.295 Angle : 0.990 12.393 12957 Z= 0.549 Chirality : 0.057 0.403 1592 Planarity : 0.008 0.064 798 Dihedral : 27.441 179.515 3785 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 6.05 % Allowed : 17.58 % Favored : 76.37 % 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: -3.16 (0.38), residues: 397 helix: -1.42 (0.46), residues: 117 sheet: -2.82 (0.57), residues: 68 loop : -2.23 (0.37), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG D 86 TYR 0.039 0.003 TYR D 388 PHE 0.033 0.005 PHE D 370 TRP 0.005 0.002 TRP D 478 HIS 0.011 0.003 HIS D 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.29 ( 8782) covalent geometry : angle 0.98984 / 0.55 (12957) hydrogen bonds : bond 0.11738 / 7.93 ( 304) hydrogen bonds : angle 4.84470 / 3.23 ( 680) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 148 LYS cc_start: 0.5832 (tttt) cc_final: 0.5585 (tptt) REVERT: D 328 LEU cc_start: 0.8936 (mt) cc_final: 0.8711 (pp) REVERT: D 436 MET cc_start: 0.7402 (mmm) cc_final: 0.7012 (mmm) REVERT: D 461 ARG cc_start: 0.7681 (mmm160) cc_final: 0.7404 (mtp85) REVERT: D 463 LYS cc_start: 0.8309 (mttm) cc_final: 0.8055 (mppt) outliers start: 21 outliers final: 9 residues processed: 85 average time/residue: 0.0828 time to fit residues: 9.4319 Evaluate side-chains 61 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 494 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 175 ASN D 300 ASN D 428 HIS D 465 GLN ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.126160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.091649 restraints weight = 13970.547| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.74 r_work: 0.3292 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.177 8782 Z= 0.234 Angle : 0.747 10.251 12957 Z= 0.430 Chirality : 0.047 0.349 1592 Planarity : 0.006 0.042 798 Dihedral : 26.898 178.917 3781 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.79 % Favored : 94.96 % Rotamer: Outliers : 5.76 % Allowed : 16.14 % Favored : 78.10 % 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: -2.20 (0.38), residues: 397 helix: -0.53 (0.45), residues: 117 sheet: -2.22 (0.58), residues: 68 loop : -1.71 (0.38), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 105 TYR 0.016 0.003 TYR D 388 PHE 0.017 0.003 PHE D 318 TRP 0.003 0.001 TRP D 161 HIS 0.011 0.003 HIS D 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.23 ( 8782) covalent geometry : angle 0.74681 / 0.43 (12957) hydrogen bonds : bond 0.08399 / 5.54 ( 304) hydrogen bonds : angle 4.55470 / 3.05 ( 680) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.108 Fit side-chains revert: symmetry clash REVERT: D 149 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.6293 (tt0) REVERT: D 371 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7839 (mtm180) REVERT: D 461 ARG cc_start: 0.7869 (mmm160) cc_final: 0.7392 (ttm-80) outliers start: 20 outliers final: 6 residues processed: 86 average time/residue: 0.0819 time to fit residues: 9.2384 Evaluate side-chains 63 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 371 ARG Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 494 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 2 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 376 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.123005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.087721 restraints weight = 14355.673| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.85 r_work: 0.3224 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.8599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 8782 Z= 0.298 Angle : 0.968 16.950 12957 Z= 0.522 Chirality : 0.053 0.382 1592 Planarity : 0.008 0.096 798 Dihedral : 26.682 178.178 3780 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 5.19 % Allowed : 17.58 % Favored : 77.23 % 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: -2.64 (0.37), residues: 397 helix: -1.44 (0.41), residues: 120 sheet: -2.26 (0.56), residues: 68 loop : -1.70 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG D 480 TYR 0.017 0.003 TYR D 365 PHE 0.078 0.005 PHE D 318 TRP 0.007 0.003 TRP D 478 HIS 0.016 0.003 HIS D 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.30 ( 8782) covalent geometry : angle 0.96777 / 0.52 (12957) hydrogen bonds : bond 0.11394 / 7.58 ( 304) hydrogen bonds : angle 4.70243 / 3.17 ( 680) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.128 Fit side-chains REVERT: D 68 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.7272 (mtm) REVERT: D 149 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7393 (tt0) outliers start: 18 outliers final: 7 residues processed: 66 average time/residue: 0.0714 time to fit residues: 6.8702 Evaluate side-chains 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 491 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 53 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 153 ASN D 492 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.116688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.080953 restraints weight = 14121.814| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.83 r_work: 0.3146 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 1.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 8782 Z= 0.412 Angle : 1.016 12.271 12957 Z= 0.559 Chirality : 0.061 0.364 1592 Planarity : 0.009 0.086 798 Dihedral : 26.712 178.775 3780 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 7.20 % Allowed : 19.60 % Favored : 73.20 % 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: -2.55 (0.38), residues: 397 helix: -1.54 (0.41), residues: 113 sheet: -1.67 (0.66), residues: 60 loop : -1.78 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG D 486 TYR 0.023 0.003 TYR D 340 PHE 0.018 0.004 PHE D 79 TRP 0.011 0.004 TRP D 478 HIS 0.012 0.003 HIS D 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00825 / 0.41 ( 8782) covalent geometry : angle 1.01614 / 0.56 (12957) hydrogen bonds : bond 0.11453 / 7.39 ( 304) hydrogen bonds : angle 4.98744 / 3.29 ( 680) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 45 time to evaluate : 0.188 Fit side-chains REVERT: D 1 MET cc_start: 0.8500 (mmp) cc_final: 0.8043 (mpp) REVERT: D 37 ARG cc_start: 0.7809 (ttp80) cc_final: 0.7020 (ttm110) REVERT: D 68 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7744 (mtm) REVERT: D 172 THR cc_start: 0.7758 (OUTLIER) cc_final: 0.6639 (m) REVERT: D 393 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8110 (pt) outliers start: 25 outliers final: 12 residues processed: 63 average time/residue: 0.0832 time to fit residues: 7.3722 Evaluate side-chains 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 492 GLN Chi-restraints excluded: chain D residue 493 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 38 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 49 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 44 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 20 optimal weight: 0.0070 chunk 0 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 376 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.121696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.086061 restraints weight = 13823.021| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.66 r_work: 0.3240 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 1.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8782 Z= 0.158 Angle : 0.698 12.532 12957 Z= 0.399 Chirality : 0.045 0.323 1592 Planarity : 0.005 0.034 798 Dihedral : 26.466 176.989 3780 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.02 % Allowed : 23.92 % Favored : 74.06 % 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: -1.66 (0.39), residues: 397 helix: -0.45 (0.43), residues: 113 sheet: -0.97 (0.67), residues: 60 loop : -1.49 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 385 TYR 0.018 0.002 TYR D 340 PHE 0.012 0.002 PHE D 370 TRP 0.007 0.001 TRP D 161 HIS 0.009 0.002 HIS D 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.16 ( 8782) covalent geometry : angle 0.69751 / 0.40 (12957) hydrogen bonds : bond 0.06656 / 4.40 ( 304) hydrogen bonds : angle 3.92829 / 2.69 ( 680) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.143 Fit side-chains REVERT: D 12 LYS cc_start: 0.8889 (tmtt) cc_final: 0.8680 (tmtt) REVERT: D 37 ARG cc_start: 0.7673 (ttp80) cc_final: 0.7026 (ttm110) REVERT: D 68 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7332 (mtt) outliers start: 7 outliers final: 4 residues processed: 42 average time/residue: 0.0667 time to fit residues: 4.0424 Evaluate side-chains 39 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 491 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.124966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.090305 restraints weight = 14330.374| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.63 r_work: 0.3345 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 1.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 8782 Z= 0.166 Angle : 0.653 10.548 12957 Z= 0.377 Chirality : 0.043 0.325 1592 Planarity : 0.005 0.033 798 Dihedral : 26.219 176.802 3780 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.02 % Allowed : 23.63 % Favored : 74.35 % 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: -1.36 (0.39), residues: 397 helix: -0.14 (0.45), residues: 113 sheet: -0.68 (0.70), residues: 60 loop : -1.37 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 110 TYR 0.019 0.001 TYR D 340 PHE 0.011 0.002 PHE D 370 TRP 0.004 0.001 TRP D 161 HIS 0.005 0.001 HIS D 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.17 ( 8782) covalent geometry : angle 0.65304 / 0.38 (12957) hydrogen bonds : bond 0.06439 / 4.22 ( 304) hydrogen bonds : angle 3.79407 / 2.63 ( 680) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.127 Fit side-chains REVERT: D 37 ARG cc_start: 0.7595 (ttp80) cc_final: 0.7123 (ttm110) REVERT: D 68 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7535 (mtt) REVERT: D 440 MET cc_start: 0.8592 (mmm) cc_final: 0.8340 (mmm) outliers start: 7 outliers final: 3 residues processed: 40 average time/residue: 0.0854 time to fit residues: 4.7650 Evaluate side-chains 33 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 449 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 130 GLN ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.127558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.094624 restraints weight = 14047.464| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.52 r_work: 0.3371 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 1.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8782 Z= 0.151 Angle : 0.625 13.036 12957 Z= 0.359 Chirality : 0.042 0.335 1592 Planarity : 0.004 0.036 798 Dihedral : 26.120 177.328 3780 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.73 % Allowed : 24.78 % Favored : 73.49 % 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: -1.22 (0.39), residues: 397 helix: 0.04 (0.44), residues: 118 sheet: -0.73 (0.68), residues: 60 loop : -1.31 (0.38), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 330 TYR 0.016 0.001 TYR D 340 PHE 0.012 0.002 PHE D 370 TRP 0.003 0.001 TRP D 161 HIS 0.007 0.002 HIS D 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.15 ( 8782) covalent geometry : angle 0.62520 / 0.36 (12957) hydrogen bonds : bond 0.05978 / 3.98 ( 304) hydrogen bonds : angle 3.66296 / 2.55 ( 680) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.191 Fit side-chains REVERT: D 37 ARG cc_start: 0.7542 (ttp80) cc_final: 0.7103 (ttm110) REVERT: D 84 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7832 (mm-30) REVERT: D 403 ASP cc_start: 0.7655 (t0) cc_final: 0.7333 (t0) outliers start: 6 outliers final: 1 residues processed: 40 average time/residue: 0.0762 time to fit residues: 4.4739 Evaluate side-chains 34 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 56 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 40 optimal weight: 10.0000 chunk 24 optimal weight: 0.0020 chunk 18 optimal weight: 0.4980 chunk 48 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.124987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.090190 restraints weight = 14207.960| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.60 r_work: 0.3351 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 1.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8782 Z= 0.158 Angle : 0.610 9.166 12957 Z= 0.355 Chirality : 0.042 0.340 1592 Planarity : 0.004 0.037 798 Dihedral : 26.030 177.071 3780 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.86 % Allowed : 25.36 % Favored : 73.78 % 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: -0.97 (0.40), residues: 397 helix: 0.24 (0.46), residues: 118 sheet: -0.60 (0.70), residues: 60 loop : -1.15 (0.38), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 110 TYR 0.017 0.001 TYR D 340 PHE 0.016 0.002 PHE D 329 TRP 0.002 0.001 TRP D 478 HIS 0.004 0.001 HIS D 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.16 ( 8782) covalent geometry : angle 0.61013 / 0.36 (12957) hydrogen bonds : bond 0.06075 / 4.00 ( 304) hydrogen bonds : angle 3.61517 / 2.55 ( 680) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.184 Fit side-chains REVERT: D 37 ARG cc_start: 0.7482 (ttp80) cc_final: 0.7091 (ttm110) REVERT: D 403 ASP cc_start: 0.7672 (t0) cc_final: 0.7231 (t0) outliers start: 3 outliers final: 3 residues processed: 39 average time/residue: 0.0885 time to fit residues: 4.9360 Evaluate side-chains 35 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 449 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 47 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 0.0270 chunk 18 optimal weight: 0.0470 chunk 55 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 2 optimal weight: 0.0040 chunk 12 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 overall best weight: 1.0152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 99 GLN D 333 HIS D 339 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.125113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.090306 restraints weight = 14141.914| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.60 r_work: 0.3349 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 1.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8782 Z= 0.159 Angle : 0.639 14.001 12957 Z= 0.362 Chirality : 0.042 0.335 1592 Planarity : 0.004 0.038 798 Dihedral : 26.007 177.472 3780 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.44 % Allowed : 25.65 % Favored : 72.91 % 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: -0.89 (0.40), residues: 397 helix: 0.43 (0.47), residues: 117 sheet: -0.78 (0.62), residues: 71 loop : -1.09 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 110 TYR 0.021 0.001 TYR D 340 PHE 0.010 0.002 PHE D 370 TRP 0.002 0.001 TRP D 161 HIS 0.016 0.002 HIS D 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 ( 8782) covalent geometry : angle 0.63936 / 0.36 (12957) hydrogen bonds : bond 0.05891 / 3.91 ( 304) hydrogen bonds : angle 3.60069 / 2.54 ( 680) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.195 Fit side-chains REVERT: D 1 MET cc_start: 0.8390 (mmm) cc_final: 0.7890 (mpp) REVERT: D 37 ARG cc_start: 0.7526 (ttp80) cc_final: 0.7156 (ttm110) REVERT: D 106 ARG cc_start: 0.8065 (ttp80) cc_final: 0.7826 (ttp-170) REVERT: D 339 HIS cc_start: 0.6774 (OUTLIER) cc_final: 0.6360 (t70) REVERT: D 403 ASP cc_start: 0.7739 (t0) cc_final: 0.7366 (t0) outliers start: 5 outliers final: 4 residues processed: 37 average time/residue: 0.1042 time to fit residues: 5.2686 Evaluate side-chains 36 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 339 HIS Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 449 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 18 optimal weight: 0.0030 chunk 40 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 65 ASN D 333 HIS D 339 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.125012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.090113 restraints weight = 14076.666| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.61 r_work: 0.3344 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 1.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8782 Z= 0.159 Angle : 0.623 12.010 12957 Z= 0.358 Chirality : 0.041 0.333 1592 Planarity : 0.004 0.038 798 Dihedral : 25.985 177.507 3780 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.44 % Allowed : 25.36 % Favored : 73.20 % 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 (0.40), residues: 397 helix: 0.38 (0.46), residues: 117 sheet: -0.57 (0.71), residues: 60 loop : -1.07 (0.38), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 110 TYR 0.013 0.001 TYR D 340 PHE 0.010 0.002 PHE D 370 TRP 0.002 0.001 TRP D 478 HIS 0.023 0.002 HIS D 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.16 ( 8782) covalent geometry : angle 0.62297 / 0.36 (12957) hydrogen bonds : bond 0.05916 / 3.90 ( 304) hydrogen bonds : angle 3.58171 / 2.53 ( 680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2548.63 seconds wall clock time: 44 minutes 11.49 seconds (2651.49 seconds total)