Starting phenix.real_space_refine on Wed Mar 12 20:04:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ctl_26994/03_2025/8ctl_26994_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ctl_26994/03_2025/8ctl_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_26994/03_2025/8ctl_26994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ctl_26994/03_2025/8ctl_26994.map" model { file = "/net/cci-nas-00/data/ceres_data/8ctl_26994/03_2025/8ctl_26994_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ctl_26994/03_2025/8ctl_26994_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.73, per 1000 atoms: 0.70 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: 2.36 Conformation dependent library (CDL) restraints added in 473.7 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: 4.09 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: 3.02 Time building geometry restraints manager: 2.72 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: 11629 2.17 - 4.35: 1182 4.35 - 6.52: 112 6.52 - 8.70: 21 8.70 - 10.87: 13 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 - 0.081: 1037 0.081 - 0.163: 443 0.163 - 0.244: 102 0.244 - 0.325: 5 0.325 - 0.406: 5 Chirality restraints: 1592 Sorted by residual: 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 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 -2.66 -2.27 -0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CA ASN D 382 " pdb=" N ASN D 382 " pdb=" C ASN D 382 " pdb=" CB ASN D 382 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.75e+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: 1.520 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.410 Find NCS groups from input model: 0.050 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4489 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= 0.596 Angle : 1.320 10.875 12957 Z= 0.934 Chirality : 0.090 0.406 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.004 0.001 TRP D 161 HIS 0.008 0.002 HIS D 373 PHE 0.012 0.002 PHE D 196 TYR 0.011 0.002 TYR D 433 ARG 0.003 0.001 ARG D 86 *********************** 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 : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 175 ASN cc_start: 0.6018 (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: 0.3076 time to fit residues: 48.7193 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 : 0.486 ------------------------------------------------------------------------------- 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 52 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 HIS D 376 GLN ** 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 = 0.3968 r_free = 0.3968 target = 0.129386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.095064 restraints weight = 13819.718| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.79 r_work: 0.3339 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6079 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 8782 Z= 0.298 Angle : 0.887 13.077 12957 Z= 0.456 Chirality : 0.046 0.365 1592 Planarity : 0.006 0.051 798 Dihedral : 27.186 179.845 3785 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.61 % Allowed : 17.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.37), residues: 397 helix: -1.41 (0.44), residues: 117 sheet: -2.89 (0.54), residues: 68 loop : -2.05 (0.38), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 161 HIS 0.020 0.003 HIS D 22 PHE 0.023 0.003 PHE D 318 TYR 0.021 0.003 TYR D 388 ARG 0.007 0.001 ARG D 330 *********************** 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 89 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 148 LYS cc_start: 0.5433 (tttt) cc_final: 0.5179 (tptt) REVERT: D 436 MET cc_start: 0.7348 (mmm) cc_final: 0.7023 (mmm) REVERT: D 463 LYS cc_start: 0.8209 (mttm) cc_final: 0.7941 (mppt) outliers start: 16 outliers final: 6 residues processed: 84 average time/residue: 0.2566 time to fit residues: 27.6053 Evaluate side-chains 61 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 341 LEU Chi-restraints excluded: chain D residue 359 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 51 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 53 GLN D 376 GLN ** D 428 HIS ** 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 = 0.3957 r_free = 0.3957 target = 0.127593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.093594 restraints weight = 14179.157| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.76 r_work: 0.3321 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.6147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 8782 Z= 0.266 Angle : 0.764 12.648 12957 Z= 0.401 Chirality : 0.043 0.507 1592 Planarity : 0.006 0.063 798 Dihedral : 26.489 177.482 3781 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.61 % Allowed : 17.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.38), residues: 397 helix: -0.80 (0.44), residues: 118 sheet: -2.45 (0.55), residues: 68 loop : -1.75 (0.38), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 478 HIS 0.013 0.003 HIS D 333 PHE 0.019 0.003 PHE D 329 TYR 0.013 0.002 TYR D 387 ARG 0.011 0.001 ARG D 33 *********************** 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 92 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 33 ARG cc_start: 0.6129 (ttp80) cc_final: 0.5323 (ptm-80) REVERT: D 461 ARG cc_start: 0.7947 (mmm160) cc_final: 0.7424 (mtt90) outliers start: 16 outliers final: 7 residues processed: 87 average time/residue: 0.2405 time to fit residues: 28.6100 Evaluate side-chains 63 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 341 LEU Chi-restraints excluded: chain D residue 359 SER 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 7 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 ASN D 376 GLN D 428 HIS ** D 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.123656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.088850 restraints weight = 14383.015| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.72 r_work: 0.3324 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 1.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 8782 Z= 0.484 Angle : 1.002 13.247 12957 Z= 0.519 Chirality : 0.053 0.475 1592 Planarity : 0.008 0.057 798 Dihedral : 26.661 175.854 3780 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 5.48 % Allowed : 17.00 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.38), residues: 397 helix: -1.04 (0.42), residues: 116 sheet: -2.16 (0.68), residues: 54 loop : -1.64 (0.38), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.003 TRP D 161 HIS 0.010 0.003 HIS D 399 PHE 0.035 0.005 PHE D 329 TYR 0.022 0.003 TYR D 340 ARG 0.011 0.001 ARG D 116 *********************** 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 66 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.574 Fit side-chains REVERT: D 309 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.6947 (mp10) REVERT: D 338 ASP cc_start: 0.8223 (m-30) cc_final: 0.8003 (m-30) REVERT: D 393 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8065 (pt) REVERT: D 440 MET cc_start: 0.8793 (tpp) cc_final: 0.8352 (mmm) outliers start: 19 outliers final: 9 residues processed: 62 average time/residue: 0.2178 time to fit residues: 18.3729 Evaluate side-chains 48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 193 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 340 TYR Chi-restraints excluded: chain D residue 393 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 24 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 130 GLN D 376 GLN D 462 ASN D 467 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.125971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.091598 restraints weight = 14116.473| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.62 r_work: 0.3374 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 1.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8782 Z= 0.226 Angle : 0.694 8.253 12957 Z= 0.371 Chirality : 0.040 0.308 1592 Planarity : 0.005 0.033 798 Dihedral : 26.199 175.330 3780 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.31 % Allowed : 18.73 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.39), residues: 397 helix: -0.28 (0.44), residues: 118 sheet: -1.74 (0.68), residues: 59 loop : -1.62 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 161 HIS 0.005 0.001 HIS D 22 PHE 0.011 0.002 PHE D 198 TYR 0.026 0.002 TYR D 340 ARG 0.004 0.001 ARG D 110 *********************** 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 49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.535 Fit side-chains REVERT: D 1 MET cc_start: 0.8422 (mmp) cc_final: 0.8155 (mmm) REVERT: D 37 ARG cc_start: 0.7565 (ttp80) cc_final: 0.7093 (ttm110) REVERT: D 59 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7571 (mt) REVERT: D 68 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.7377 (mtt) REVERT: D 338 ASP cc_start: 0.8203 (m-30) cc_final: 0.7918 (t70) REVERT: D 402 MET cc_start: 0.8415 (mmm) cc_final: 0.8180 (mmt) outliers start: 8 outliers final: 3 residues processed: 47 average time/residue: 0.1624 time to fit residues: 11.3982 Evaluate side-chains 40 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 449 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 37 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.0870 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 333 HIS D 467 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.125634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.091191 restraints weight = 14096.322| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.62 r_work: 0.3358 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 1.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8782 Z= 0.222 Angle : 0.653 8.253 12957 Z= 0.351 Chirality : 0.038 0.304 1592 Planarity : 0.005 0.038 798 Dihedral : 25.972 175.654 3780 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.88 % Allowed : 20.46 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.41), residues: 397 helix: 0.47 (0.47), residues: 118 sheet: -1.76 (0.67), residues: 60 loop : -1.26 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 478 HIS 0.013 0.002 HIS D 333 PHE 0.014 0.002 PHE D 318 TYR 0.024 0.002 TYR D 340 ARG 0.004 0.000 ARG D 371 *********************** 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 48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.503 Fit side-chains REVERT: D 37 ARG cc_start: 0.7568 (ttp80) cc_final: 0.7130 (ttm110) REVERT: D 333 HIS cc_start: 0.7217 (OUTLIER) cc_final: 0.6721 (m90) REVERT: D 402 MET cc_start: 0.8561 (mmm) cc_final: 0.8271 (mmt) REVERT: D 403 ASP cc_start: 0.7802 (t0) cc_final: 0.7157 (t0) REVERT: D 405 LYS cc_start: 0.8437 (mmmm) cc_final: 0.8185 (mptt) REVERT: D 440 MET cc_start: 0.8615 (mmm) cc_final: 0.8367 (mmm) REVERT: D 493 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8551 (tp) outliers start: 10 outliers final: 5 residues processed: 45 average time/residue: 0.1810 time to fit residues: 11.7109 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 : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 333 HIS Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 449 GLU 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 23 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.125915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.091463 restraints weight = 14210.928| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.63 r_work: 0.3370 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 1.2853 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= 0.200 Angle : 0.635 10.848 12957 Z= 0.341 Chirality : 0.038 0.297 1592 Planarity : 0.004 0.041 798 Dihedral : 25.899 175.959 3780 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.73 % Allowed : 22.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.41), residues: 397 helix: 0.73 (0.48), residues: 119 sheet: -1.47 (0.68), residues: 61 loop : -1.05 (0.40), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 478 HIS 0.013 0.002 HIS D 333 PHE 0.019 0.002 PHE D 329 TYR 0.008 0.001 TYR D 5 ARG 0.002 0.000 ARG D 330 *********************** 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 45 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: D 37 ARG cc_start: 0.7527 (ttp80) cc_final: 0.7034 (ttm110) REVERT: D 333 HIS cc_start: 0.7297 (OUTLIER) cc_final: 0.6729 (m-70) REVERT: D 335 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8630 (mp) REVERT: D 402 MET cc_start: 0.8567 (mmm) cc_final: 0.8321 (mmt) REVERT: D 403 ASP cc_start: 0.7786 (t0) cc_final: 0.7273 (t0) REVERT: D 405 LYS cc_start: 0.8368 (mmmm) cc_final: 0.8159 (mptt) REVERT: D 440 MET cc_start: 0.8633 (mmm) cc_final: 0.8384 (mmm) outliers start: 6 outliers final: 3 residues processed: 43 average time/residue: 0.1951 time to fit residues: 11.7490 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 : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 333 HIS Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 426 VAL 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 6 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 333 HIS ** 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 = 0.3951 r_free = 0.3951 target = 0.121110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.086061 restraints weight = 14361.971| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.66 r_work: 0.3275 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 1.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8782 Z= 0.318 Angle : 0.699 9.820 12957 Z= 0.373 Chirality : 0.042 0.325 1592 Planarity : 0.005 0.042 798 Dihedral : 25.898 176.192 3780 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.02 % Allowed : 21.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.40), residues: 397 helix: 0.56 (0.47), residues: 119 sheet: -1.41 (0.68), residues: 61 loop : -1.02 (0.39), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP D 161 HIS 0.005 0.001 HIS D 333 PHE 0.015 0.002 PHE D 79 TYR 0.013 0.002 TYR D 340 ARG 0.005 0.001 ARG D 461 *********************** 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 45 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: D 36 GLU cc_start: 0.8077 (tp30) cc_final: 0.7868 (tp30) REVERT: D 37 ARG cc_start: 0.7654 (ttp80) cc_final: 0.6964 (ttm110) REVERT: D 106 ARG cc_start: 0.8114 (ttp80) cc_final: 0.7558 (ttt90) REVERT: D 335 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8631 (mp) REVERT: D 403 ASP cc_start: 0.7769 (t0) cc_final: 0.7307 (t0) REVERT: D 440 MET cc_start: 0.8652 (mmm) cc_final: 0.8428 (mmm) REVERT: D 493 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8503 (tp) outliers start: 7 outliers final: 4 residues processed: 43 average time/residue: 0.2731 time to fit residues: 15.3279 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 : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 430 SER 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 48 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 20 optimal weight: 0.0270 chunk 21 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 99 GLN ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 467 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.124732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.090000 restraints weight = 14293.430| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.63 r_work: 0.3345 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 1.3867 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= 0.190 Angle : 0.630 11.383 12957 Z= 0.339 Chirality : 0.038 0.325 1592 Planarity : 0.004 0.040 798 Dihedral : 25.799 176.255 3780 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.44 % Allowed : 22.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.41), residues: 397 helix: 0.89 (0.47), residues: 118 sheet: -1.10 (0.70), residues: 60 loop : -0.98 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 478 HIS 0.004 0.001 HIS D 373 PHE 0.013 0.002 PHE D 329 TYR 0.016 0.001 TYR D 340 ARG 0.002 0.000 ARG D 131 *********************** 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 43 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: D 37 ARG cc_start: 0.7597 (ttp80) cc_final: 0.7055 (ttm110) REVERT: D 106 ARG cc_start: 0.8061 (ttp80) cc_final: 0.7536 (ttt90) REVERT: D 335 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8568 (mp) REVERT: D 402 MET cc_start: 0.8441 (mmm) cc_final: 0.7714 (tpp) REVERT: D 403 ASP cc_start: 0.7713 (t0) cc_final: 0.7339 (t0) REVERT: D 440 MET cc_start: 0.8675 (mmm) cc_final: 0.8458 (mmm) REVERT: D 493 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8528 (tp) outliers start: 5 outliers final: 2 residues processed: 42 average time/residue: 0.2341 time to fit residues: 13.2693 Evaluate side-chains 39 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 493 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 19 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.124328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.089535 restraints weight = 14062.099| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.65 r_work: 0.3338 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 1.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8782 Z= 0.209 Angle : 0.619 8.130 12957 Z= 0.336 Chirality : 0.038 0.300 1592 Planarity : 0.004 0.040 798 Dihedral : 25.741 178.032 3780 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.86 % Allowed : 22.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.41), residues: 397 helix: 0.97 (0.48), residues: 119 sheet: -0.98 (0.70), residues: 60 loop : -0.94 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 478 HIS 0.003 0.001 HIS D 373 PHE 0.014 0.002 PHE D 329 TYR 0.009 0.001 TYR D 5 ARG 0.003 0.000 ARG D 110 ********************** 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 : 0.489 Fit side-chains revert: symmetry clash REVERT: D 106 ARG cc_start: 0.8084 (ttp80) cc_final: 0.7561 (ttt90) REVERT: D 335 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8528 (mp) REVERT: D 402 MET cc_start: 0.8449 (mmm) cc_final: 0.7745 (tpp) REVERT: D 403 ASP cc_start: 0.7760 (t0) cc_final: 0.7346 (t0) REVERT: D 440 MET cc_start: 0.8639 (mmm) cc_final: 0.8428 (mmm) REVERT: D 493 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8532 (tp) outliers start: 3 outliers final: 1 residues processed: 36 average time/residue: 0.2358 time to fit residues: 11.4396 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 : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 493 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.0050 chunk 54 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 chunk 49 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 333 HIS D 467 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.126507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.091868 restraints weight = 14188.451| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.63 r_work: 0.3377 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 1.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8782 Z= 0.173 Angle : 0.596 7.658 12957 Z= 0.324 Chirality : 0.036 0.275 1592 Planarity : 0.004 0.041 798 Dihedral : 25.694 179.581 3780 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.44 % Allowed : 22.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.41), residues: 397 helix: 1.11 (0.47), residues: 119 sheet: -0.96 (0.68), residues: 61 loop : -0.80 (0.40), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 478 HIS 0.003 0.001 HIS D 373 PHE 0.014 0.002 PHE D 329 TYR 0.017 0.001 TYR D 340 ARG 0.003 0.000 ARG D 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5917.03 seconds wall clock time: 102 minutes 21.99 seconds (6141.99 seconds total)