Starting phenix.real_space_refine on Fri Sep 11 06:34:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ctl_26994/09_2026/8ctl_26994_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ctl_26994/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ctl_26994/09_2026/8ctl_26994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ctl_26994/09_2026/8ctl_26994.map" model { file = "/net/cci-nas-00/data/ceres_data/8ctl_26994/09_2026/8ctl_26994_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ctl_26994/09_2026/8ctl_26994_neut.cif" } 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-2.2.1-6174/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: 1.51, per 1000 atoms: 0.19 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: 0.95 Conformation dependent library (CDL) restraints added in 130.0 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: 1.08 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: 1.56 Time building geometry restraints manager: 1.15 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: 11798 2.17 - 4.35: 1010 4.35 - 6.52: 114 6.52 - 8.70: 21 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: 1239 0.093 - 0.185: 301 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.610 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.220 ------------------------------------------------------------------------------- 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= 0.708 Angle : 1.270 10.875 12957 Z= 0.913 Chirality : 0.082 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 0.00945 / 0.71 ( 8782) covalent geometry : angle 1.27042 / 0.91 (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 : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 175 ASN cc_start: 0.6017 (m-40) cc_final: 0.5701 (m-40) REVERT: D 443 SER cc_start: 0.6737 (m) cc_final: 0.6075 (t) REVERT: D 470 VAL cc_start: 0.5463 (OUTLIER) cc_final: 0.5219 (t) outliers start: 25 outliers final: 3 residues processed: 129 average time/residue: 0.1254 time to fit residues: 20.0557 Evaluate side-chains 78 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.170 ------------------------------------------------------------------------------- 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: 3.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 56 optimal weight: 30.0000 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN D 373 HIS ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 462 ASN D 465 GLN D 487 ASN D 492 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.128368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.094104 restraints weight = 14058.388| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.72 r_work: 0.3326 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6194 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 8782 Z= 0.267 Angle : 1.050 12.036 12957 Z= 0.547 Chirality : 0.069 0.765 1592 Planarity : 0.008 0.053 798 Dihedral : 27.388 179.643 3785 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 6.34 % Allowed : 17.29 % 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: -3.08 (0.38), residues: 397 helix: -1.35 (0.46), residues: 117 sheet: -2.81 (0.56), residues: 68 loop : -2.18 (0.37), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 86 TYR 0.019 0.003 TYR D 388 PHE 0.029 0.005 PHE D 370 TRP 0.004 0.001 TRP D 478 HIS 0.013 0.003 HIS D 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.27 ( 8782) covalent geometry : angle 1.04954 / 0.55 (12957) hydrogen bonds : bond 0.10669 / 7.24 ( 304) hydrogen bonds : angle 4.78550 / 3.19 ( 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 94 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 148 LYS cc_start: 0.5574 (tttt) cc_final: 0.5355 (tptt) REVERT: D 436 MET cc_start: 0.7326 (mmm) cc_final: 0.6878 (mmm) outliers start: 22 outliers final: 9 residues processed: 84 average time/residue: 0.0799 time to fit residues: 9.1596 Evaluate side-chains 59 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.166 ------------------------------------------------------------------------------- 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: 0.9990 chunk 43 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 21 optimal weight: 0.0670 chunk 16 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 46 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 53 GLN D 175 ASN D 300 ASN D 324 GLN D 428 HIS D 465 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.127908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.093520 restraints weight = 13906.060| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.73 r_work: 0.3326 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 8782 Z= 0.180 Angle : 0.733 9.978 12957 Z= 0.407 Chirality : 0.051 0.650 1592 Planarity : 0.005 0.034 798 Dihedral : 26.835 179.373 3781 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.17 % Allowed : 18.73 % 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: -2.07 (0.39), residues: 397 helix: -0.40 (0.45), residues: 118 sheet: -2.24 (0.59), residues: 68 loop : -1.61 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 116 TYR 0.012 0.002 TYR D 388 PHE 0.012 0.002 PHE D 40 TRP 0.003 0.001 TRP D 161 HIS 0.013 0.002 HIS D 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.18 ( 8782) covalent geometry : angle 0.73259 / 0.41 (12957) hydrogen bonds : bond 0.08131 / 5.41 ( 304) hydrogen bonds : angle 4.24716 / 2.87 ( 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 72 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 33 ARG cc_start: 0.5802 (ttp80) cc_final: 0.5174 (ptm-80) REVERT: D 148 LYS cc_start: 0.5776 (tttt) cc_final: 0.5395 (tptt) REVERT: D 338 ASP cc_start: 0.6365 (m-30) cc_final: 0.6026 (m-30) REVERT: D 461 ARG cc_start: 0.7424 (mmm-85) cc_final: 0.7208 (mtp85) outliers start: 11 outliers final: 7 residues processed: 67 average time/residue: 0.0887 time to fit residues: 7.8932 Evaluate side-chains 66 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 341 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: 4.9990 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 194 ASN D 376 GLN ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.124013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.089499 restraints weight = 14441.770| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.79 r_work: 0.3259 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.7687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 8782 Z= 0.311 Angle : 0.991 20.241 12957 Z= 0.515 Chirality : 0.059 0.519 1592 Planarity : 0.008 0.084 798 Dihedral : 26.572 179.679 3780 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 6.34 % Allowed : 15.27 % Favored : 78.39 % 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: -2.60 (0.37), residues: 397 helix: -1.25 (0.41), residues: 118 sheet: -2.15 (0.57), residues: 68 loop : -1.83 (0.39), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG D 480 TYR 0.015 0.003 TYR D 365 PHE 0.036 0.004 PHE D 318 TRP 0.045 0.009 TRP D 478 HIS 0.018 0.003 HIS D 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.31 ( 8782) covalent geometry : angle 0.99111 / 0.52 (12957) hydrogen bonds : bond 0.09948 / 6.62 ( 304) hydrogen bonds : angle 4.58804 / 3.12 ( 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 86 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 178 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7577 (mttp) REVERT: D 328 LEU cc_start: 0.9085 (mt) cc_final: 0.8790 (mt) REVERT: D 461 ARG cc_start: 0.8049 (mmm-85) cc_final: 0.7753 (ttm-80) outliers start: 22 outliers final: 8 residues processed: 81 average time/residue: 0.1002 time to fit residues: 10.5053 Evaluate side-chains 58 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.167 ------------------------------------------------------------------------------- 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 52 THR Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 178 LYS 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 494 TYR 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: 1.9990 chunk 59 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 20.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 194 ASN D 376 GLN D 492 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.121307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.085859 restraints weight = 14420.600| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.66 r_work: 0.3246 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 1.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.101 8782 Z= 0.378 Angle : 1.099 16.823 12957 Z= 0.579 Chirality : 0.066 0.621 1592 Planarity : 0.011 0.137 798 Dihedral : 26.719 176.049 3780 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 7.49 % Allowed : 18.16 % 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: -2.64 (0.37), residues: 397 helix: -1.29 (0.41), residues: 117 sheet: -1.80 (0.65), residues: 60 loop : -2.00 (0.37), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG D 480 TYR 0.025 0.003 TYR D 484 PHE 0.025 0.004 PHE D 79 TRP 0.022 0.005 TRP D 478 HIS 0.013 0.003 HIS D 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00753 / 0.38 ( 8782) covalent geometry : angle 1.09941 / 0.58 (12957) hydrogen bonds : bond 0.11656 / 7.68 ( 304) hydrogen bonds : angle 5.06510 / 3.35 ( 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 74 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 48 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: D 1 MET cc_start: 0.8427 (mmp) cc_final: 0.8010 (mpp) REVERT: D 37 ARG cc_start: 0.7861 (ttp80) cc_final: 0.6750 (ttm110) REVERT: D 393 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8323 (pt) REVERT: D 403 ASP cc_start: 0.7650 (t0) cc_final: 0.7111 (t0) REVERT: D 440 MET cc_start: 0.8831 (tpp) cc_final: 0.8354 (mmm) outliers start: 26 outliers final: 10 residues processed: 67 average time/residue: 0.0895 time to fit residues: 7.9390 Evaluate side-chains 47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.165 ------------------------------------------------------------------------------- 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 59 ILE Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 394 VAL 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: 0.9980 chunk 10 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 30 optimal weight: 0.5980 chunk 44 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 154 ASN D 369 GLN D 492 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.123001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.087639 restraints weight = 13864.528| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.67 r_work: 0.3273 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 1.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8782 Z= 0.163 Angle : 0.702 9.625 12957 Z= 0.394 Chirality : 0.048 0.561 1592 Planarity : 0.005 0.031 798 Dihedral : 26.352 176.564 3780 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.73 % Allowed : 22.77 % Favored : 75.50 % 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: -1.84 (0.38), residues: 397 helix: -0.34 (0.44), residues: 117 sheet: -1.26 (0.66), residues: 60 loop : -1.72 (0.37), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 372 TYR 0.013 0.002 TYR D 340 PHE 0.009 0.002 PHE D 370 TRP 0.006 0.002 TRP D 161 HIS 0.003 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 ( 8782) covalent geometry : angle 0.70171 / 0.39 (12957) hydrogen bonds : bond 0.07011 / 4.71 ( 304) hydrogen bonds : angle 4.08165 / 2.76 ( 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 43 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.8428 (mmp) cc_final: 0.8061 (mpp) REVERT: D 37 ARG cc_start: 0.7678 (ttp80) cc_final: 0.7098 (ttm110) REVERT: D 403 ASP cc_start: 0.7853 (t0) cc_final: 0.7310 (t0) outliers start: 6 outliers final: 6 residues processed: 43 average time/residue: 0.0874 time to fit residues: 5.1982 Evaluate side-chains 38 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 492 GLN Chi-restraints excluded: chain D residue 493 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 19 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 46 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.121275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.085855 restraints weight = 14047.398| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.71 r_work: 0.3219 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 1.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8782 Z= 0.169 Angle : 0.679 8.913 12957 Z= 0.376 Chirality : 0.047 0.562 1592 Planarity : 0.005 0.041 798 Dihedral : 26.200 177.237 3780 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.31 % Allowed : 21.61 % Favored : 76.08 % 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: -1.48 (0.39), residues: 397 helix: 0.08 (0.45), residues: 117 sheet: -0.98 (0.68), residues: 60 loop : -1.59 (0.37), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 372 TYR 0.010 0.001 TYR D 484 PHE 0.010 0.001 PHE D 370 TRP 0.003 0.001 TRP D 478 HIS 0.007 0.001 HIS D 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.17 ( 8782) covalent geometry : angle 0.67877 / 0.38 (12957) hydrogen bonds : bond 0.06678 / 4.38 ( 304) hydrogen bonds : angle 3.87652 / 2.65 ( 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 41 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: D 1 MET cc_start: 0.8394 (mmp) cc_final: 0.8152 (mmm) REVERT: D 37 ARG cc_start: 0.7691 (ttp80) cc_final: 0.7111 (ttm110) REVERT: D 403 ASP cc_start: 0.7947 (t0) cc_final: 0.7444 (t0) outliers start: 8 outliers final: 6 residues processed: 39 average time/residue: 0.0705 time to fit residues: 4.0893 Evaluate side-chains 39 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 491 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 48 optimal weight: 9.9990 chunk 37 optimal weight: 0.0980 chunk 46 optimal weight: 20.0000 chunk 24 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3962 r_free = 0.3962 target = 0.124723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.089747 restraints weight = 13801.473| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.67 r_work: 0.3307 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 1.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 8782 Z= 0.137 Angle : 0.619 8.772 12957 Z= 0.352 Chirality : 0.044 0.533 1592 Planarity : 0.004 0.035 798 Dihedral : 26.104 177.900 3780 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.31 % Allowed : 21.90 % Favored : 75.79 % 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: -1.12 (0.39), residues: 397 helix: 0.49 (0.46), residues: 117 sheet: -0.76 (0.71), residues: 55 loop : -1.44 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 372 TYR 0.009 0.001 TYR D 484 PHE 0.006 0.001 PHE D 370 TRP 0.003 0.001 TRP D 161 HIS 0.004 0.001 HIS D 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.14 ( 8782) covalent geometry : angle 0.61935 / 0.35 (12957) hydrogen bonds : bond 0.05980 / 3.99 ( 304) hydrogen bonds : angle 3.64404 / 2.54 ( 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 43 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.180 Fit side-chains REVERT: D 1 MET cc_start: 0.8424 (mmp) cc_final: 0.8211 (mmm) REVERT: D 37 ARG cc_start: 0.7650 (ttp80) cc_final: 0.7129 (ttm110) REVERT: D 403 ASP cc_start: 0.7804 (t0) cc_final: 0.7217 (t0) outliers start: 8 outliers final: 6 residues processed: 42 average time/residue: 0.0684 time to fit residues: 4.3236 Evaluate side-chains 36 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 493 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 56 optimal weight: 30.0000 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 48 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 130 GLN ** D 492 GLN ** 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 = 0.3926 r_free = 0.3926 target = 0.121931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.086868 restraints weight = 13951.056| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.63 r_work: 0.3253 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 1.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8782 Z= 0.175 Angle : 0.647 8.812 12957 Z= 0.362 Chirality : 0.046 0.553 1592 Planarity : 0.005 0.034 798 Dihedral : 26.027 178.019 3780 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.44 % Allowed : 23.34 % Favored : 75.22 % 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: -1.00 (0.39), residues: 397 helix: 0.38 (0.46), residues: 118 sheet: -0.60 (0.73), residues: 55 loop : -1.27 (0.37), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 372 TYR 0.010 0.001 TYR D 5 PHE 0.018 0.002 PHE D 318 TRP 0.004 0.001 TRP D 478 HIS 0.003 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.17 ( 8782) covalent geometry : angle 0.64734 / 0.36 (12957) hydrogen bonds : bond 0.06473 / 4.21 ( 304) hydrogen bonds : angle 3.71237 / 2.58 ( 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 42 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.190 Fit side-chains REVERT: D 37 ARG cc_start: 0.7715 (ttp80) cc_final: 0.7190 (ttm110) REVERT: D 106 ARG cc_start: 0.8099 (ttp80) cc_final: 0.7593 (ttt90) REVERT: D 403 ASP cc_start: 0.7852 (t0) cc_final: 0.7514 (t0) REVERT: D 405 LYS cc_start: 0.8486 (mmmm) cc_final: 0.8269 (mptt) outliers start: 5 outliers final: 5 residues processed: 40 average time/residue: 0.0854 time to fit residues: 4.8303 Evaluate side-chains 41 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 425 THR 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: 9.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 55 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.127297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.093168 restraints weight = 14194.061| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.60 r_work: 0.3396 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 1.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8782 Z= 0.138 Angle : 0.615 13.351 12957 Z= 0.345 Chirality : 0.043 0.534 1592 Planarity : 0.004 0.035 798 Dihedral : 25.973 177.950 3780 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.86 % Allowed : 25.07 % 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: -0.69 (0.40), residues: 397 helix: 0.80 (0.47), residues: 117 sheet: -0.42 (0.75), residues: 55 loop : -1.16 (0.38), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 110 TYR 0.008 0.001 TYR D 340 PHE 0.013 0.002 PHE D 318 TRP 0.002 0.001 TRP D 478 HIS 0.003 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 ( 8782) covalent geometry : angle 0.61496 / 0.34 (12957) hydrogen bonds : bond 0.05740 / 3.82 ( 304) hydrogen bonds : angle 3.50271 / 2.46 ( 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 37 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: D 37 ARG cc_start: 0.7584 (ttp80) cc_final: 0.7189 (ttm110) REVERT: D 106 ARG cc_start: 0.8033 (ttp80) cc_final: 0.7572 (ttt90) REVERT: D 403 ASP cc_start: 0.7731 (t0) cc_final: 0.7312 (t0) outliers start: 3 outliers final: 3 residues processed: 37 average time/residue: 0.1032 time to fit residues: 5.1366 Evaluate side-chains 36 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 320 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: 0.7980 chunk 8 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 154 ASN D 376 GLN ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.126066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.091823 restraints weight = 14103.141| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.59 r_work: 0.3371 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 1.3174 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= 0.149 Angle : 0.612 10.731 12957 Z= 0.343 Chirality : 0.044 0.540 1592 Planarity : 0.004 0.036 798 Dihedral : 25.911 178.056 3780 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.44 % Allowed : 24.21 % 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: -0.66 (0.40), residues: 397 helix: 0.76 (0.47), residues: 117 sheet: -0.61 (0.71), residues: 60 loop : -1.04 (0.38), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 63 TYR 0.010 0.001 TYR D 484 PHE 0.009 0.002 PHE D 79 TRP 0.003 0.001 TRP D 478 HIS 0.003 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 ( 8782) covalent geometry : angle 0.61232 / 0.34 (12957) hydrogen bonds : bond 0.05949 / 3.89 ( 304) hydrogen bonds : angle 3.56293 / 2.49 ( 680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2461.67 seconds wall clock time: 42 minutes 39.97 seconds (2559.97 seconds total)