Starting phenix.real_space_refine on Thu Aug 6 19:28:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cf1_45526/08_2026/9cf1_45526_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cf1_45526/08_2026/9cf1_45526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cf1_45526/08_2026/9cf1_45526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cf1_45526/08_2026/9cf1_45526.map" model { file = "/net/cci-nas-00/data/ceres_data/9cf1_45526/08_2026/9cf1_45526_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cf1_45526/08_2026/9cf1_45526_neut.cif" } resolution = 3.52 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= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 82 5.49 5 S 35 5.16 5 C 5416 2.51 5 N 1570 2.21 5 O 1836 1.98 5 H 8199 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17138 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2426 Classifications: {'peptide': 162} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 151} Chain: "N" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 349 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "P" Number of atoms: 12097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 12097 Classifications: {'peptide': 726} Link IDs: {'PTRANS': 26, 'TRANS': 699} Chain breaks: 1 Chain: "T" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 639 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "W" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1627 Classifications: {'DNA': 10, 'RNA': 41} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 17, 'rna3p_pyr': 13} Link IDs: {'rna2p': 11, 'rna3p': 39} Time building chain proxies: 2.97, per 1000 atoms: 0.17 Number of scatterers: 17138 At special positions: 0 Unit cell: (80.025, 118.8, 122.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 35 16.00 P 82 15.00 O 1836 8.00 N 1570 7.00 C 5416 6.00 H 8199 1.00 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: 1.52 Conformation dependent library (CDL) restraints added in 515.2 milliseconds 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1684 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 7 sheets defined 53.8% alpha, 11.8% beta 28 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 2.78 Creating SS restraints... Processing helix chain 'B' and resid 27 through 40 Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 133 through 143 Processing helix chain 'P' and resid 114 through 118 Processing helix chain 'P' and resid 119 through 121 No H-bonds generated for 'chain 'P' and resid 119 through 121' Processing helix chain 'P' and resid 122 through 155 removed outlier: 3.633A pdb=" N LEU P 135 " --> pdb=" O HIS P 131 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 163 Processing helix chain 'P' and resid 165 through 176 removed outlier: 3.726A pdb=" N LEU P 176 " --> pdb=" O VAL P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 187 Processing helix chain 'P' and resid 188 through 209 removed outlier: 3.837A pdb=" N HIS P 201 " --> pdb=" O LEU P 197 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP P 203 " --> pdb=" O GLY P 199 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ALA P 204 " --> pdb=" O LYS P 200 " (cutoff:3.500A) Processing helix chain 'P' and resid 219 through 254 removed outlier: 3.615A pdb=" N LYS P 229 " --> pdb=" O TYR P 225 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA P 240 " --> pdb=" O ASN P 236 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLY P 243 " --> pdb=" O LYS P 239 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ASN P 244 " --> pdb=" O ALA P 240 " (cutoff:3.500A) Processing helix chain 'P' and resid 255 through 270 Processing helix chain 'P' and resid 273 through 285 Processing helix chain 'P' and resid 285 through 298 Processing helix chain 'P' and resid 308 through 321 Processing helix chain 'P' and resid 328 through 331 Processing helix chain 'P' and resid 332 through 340 removed outlier: 3.707A pdb=" N VAL P 338 " --> pdb=" O PHE P 334 " (cutoff:3.500A) Processing helix chain 'P' and resid 341 through 343 No H-bonds generated for 'chain 'P' and resid 341 through 343' Processing helix chain 'P' and resid 344 through 358 Processing helix chain 'P' and resid 381 through 388 Processing helix chain 'P' and resid 396 through 398 No H-bonds generated for 'chain 'P' and resid 396 through 398' Processing helix chain 'P' and resid 399 through 408 removed outlier: 3.995A pdb=" N VAL P 407 " --> pdb=" O ALA P 403 " (cutoff:3.500A) Processing helix chain 'P' and resid 412 through 416 Processing helix chain 'P' and resid 419 through 423 Processing helix chain 'P' and resid 466 through 470 Processing helix chain 'P' and resid 471 through 478 Processing helix chain 'P' and resid 512 through 516 Processing helix chain 'P' and resid 516 through 530 Processing helix chain 'P' and resid 531 through 543 Processing helix chain 'P' and resid 550 through 574 removed outlier: 3.553A pdb=" N VAL P 564 " --> pdb=" O ALA P 560 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ASP P 566 " --> pdb=" O ALA P 562 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE P 567 " --> pdb=" O SER P 563 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU P 568 " --> pdb=" O VAL P 564 " (cutoff:3.500A) Processing helix chain 'P' and resid 622 through 639 removed outlier: 4.208A pdb=" N LYS P 626 " --> pdb=" O ASP P 622 " (cutoff:3.500A) Processing helix chain 'P' and resid 640 through 645 Processing helix chain 'P' and resid 648 through 665 Processing helix chain 'P' and resid 668 through 680 removed outlier: 3.866A pdb=" N LYS P 672 " --> pdb=" O GLU P 668 " (cutoff:3.500A) Processing helix chain 'P' and resid 681 through 684 Processing helix chain 'P' and resid 686 through 713 removed outlier: 3.505A pdb=" N LYS P 711 " --> pdb=" O LYS P 707 " (cutoff:3.500A) Processing helix chain 'P' and resid 737 through 747 removed outlier: 3.734A pdb=" N ARG P 741 " --> pdb=" O ASN P 737 " (cutoff:3.500A) Processing helix chain 'P' and resid 782 through 787 removed outlier: 4.159A pdb=" N LYS P 786 " --> pdb=" O HIS P 782 " (cutoff:3.500A) Processing helix chain 'P' and resid 800 through 806 removed outlier: 4.207A pdb=" N GLN P 806 " --> pdb=" O CYS P 803 " (cutoff:3.500A) Processing helix chain 'P' and resid 818 through 837 Processing helix chain 'P' and resid 840 through 844 Processing sheet with id=AA1, first strand: chain 'B' and resid 53 through 55 removed outlier: 4.104A pdb=" N LEU B 95 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU B 96 " --> pdb=" O PHE B 127 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL B 19 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA B 10 " --> pdb=" O PRO B 14 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY B 16 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS B 158 " --> pdb=" O ASP B 7 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU B 9 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL B 156 " --> pdb=" O GLU B 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 107 through 113 removed outlier: 3.858A pdb=" N LEU P 440 " --> pdb=" O THR P 429 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N THR P 429 " --> pdb=" O LEU P 440 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N GLN P 442 " --> pdb=" O GLN P 427 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLN P 427 " --> pdb=" O GLN P 442 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 177 through 178 Processing sheet with id=AA4, first strand: chain 'P' and resid 507 through 511 removed outlier: 6.222A pdb=" N LEU P 719 " --> pdb=" O TYR P 752 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE P 754 " --> pdb=" O LEU P 719 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU P 721 " --> pdb=" O ILE P 754 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 591 through 593 removed outlier: 6.207A pdb=" N TYR P 601 " --> pdb=" O PHE P 605 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N PHE P 605 " --> pdb=" O TYR P 601 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 770 through 771 Processing sheet with id=AA7, first strand: chain 'P' and resid 775 through 777 364 hydrogen bonds defined for protein. 1023 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 144 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 3.82 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.92 - 1.10: 8182 1.10 - 1.28: 1247 1.28 - 1.46: 3374 1.46 - 1.64: 4645 1.64 - 1.82: 53 Bond restraints: 17501 Sorted by residual: bond pdb=" C8 DA W 48 " pdb=" H8 DA W 48 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" C5 U W 31 " pdb=" H5 U W 31 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N CYS P 792 " pdb=" H CYS P 792 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N6 DA W 46 " pdb=" H61 DA W 46 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" CE3 TRP P 724 " pdb=" HE3 TRP P 724 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 ... (remaining 17496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 27738 2.85 - 5.70: 3155 5.70 - 8.55: 714 8.55 - 11.40: 21 11.40 - 14.25: 14 Bond angle restraints: 31642 Sorted by residual: angle pdb=" O4' C W 18 " pdb=" C1' C W 18 " pdb=" N1 C W 18 " ideal model delta sigma weight residual 108.20 117.72 -9.52 8.00e-01 1.56e+00 1.42e+02 angle pdb=" O4' A W 16 " pdb=" C1' A W 16 " pdb=" N9 A W 16 " ideal model delta sigma weight residual 108.20 116.93 -8.73 8.00e-01 1.56e+00 1.19e+02 angle pdb=" N6 A W 28 " pdb=" C6 A W 28 " pdb=" N1 A W 28 " ideal model delta sigma weight residual 118.60 112.12 6.48 6.00e-01 2.78e+00 1.17e+02 angle pdb=" O4' U W 17 " pdb=" C1' U W 17 " pdb=" N1 U W 17 " ideal model delta sigma weight residual 108.20 116.84 -8.64 8.00e-01 1.56e+00 1.17e+02 angle pdb=" O5' A W 33 " pdb=" C5' A W 33 " pdb=" C4' A W 33 " ideal model delta sigma weight residual 109.40 117.70 -8.30 8.00e-01 1.56e+00 1.08e+02 ... (remaining 31637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 7584 35.44 - 70.88: 459 70.88 - 106.32: 30 106.32 - 141.75: 9 141.75 - 177.19: 7 Dihedral angle restraints: 8089 sinusoidal: 4963 harmonic: 3126 Sorted by residual: dihedral pdb=" C5' A W 32 " pdb=" C4' A W 32 " pdb=" C3' A W 32 " pdb=" O3' A W 32 " ideal model delta sinusoidal sigma weight residual 147.00 75.55 71.45 1 8.00e+00 1.56e-02 1.02e+02 dihedral pdb=" O4' A W 32 " pdb=" C4' A W 32 " pdb=" C3' A W 32 " pdb=" C2' A W 32 " ideal model delta sinusoidal sigma weight residual 24.00 -38.49 62.49 1 8.00e+00 1.56e-02 8.07e+01 dihedral pdb=" C5' A W 29 " pdb=" C4' A W 29 " pdb=" C3' A W 29 " pdb=" O3' A W 29 " ideal model delta sinusoidal sigma weight residual 147.00 88.16 58.84 1 8.00e+00 1.56e-02 7.24e+01 ... (remaining 8086 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1012 0.094 - 0.188: 348 0.188 - 0.281: 59 0.281 - 0.375: 12 0.375 - 0.469: 3 Chirality restraints: 1434 Sorted by residual: chirality pdb=" CA TYR P 613 " pdb=" N TYR P 613 " pdb=" C TYR P 613 " pdb=" CB TYR P 613 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.49e+00 chirality pdb=" C3' DT T 0 " pdb=" C4' DT T 0 " pdb=" O3' DT T 0 " pdb=" C2' DT T 0 " both_signs ideal model delta sigma weight residual False -2.73 -2.27 -0.46 2.00e-01 2.50e+01 5.32e+00 chirality pdb=" C3' U W 31 " pdb=" C4' U W 31 " pdb=" O3' U W 31 " pdb=" C2' U W 31 " both_signs ideal model delta sigma weight residual False -2.74 -2.33 -0.41 2.00e-01 2.50e+01 4.24e+00 ... (remaining 1431 not shown) Planarity restraints: 2263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C W 18 " -0.576 2.00e-02 2.50e+03 2.48e-01 1.69e+03 pdb=" N1 C W 18 " 0.014 2.00e-02 2.50e+03 pdb=" C2 C W 18 " 0.110 2.00e-02 2.50e+03 pdb=" O2 C W 18 " 0.375 2.00e-02 2.50e+03 pdb=" N3 C W 18 " -0.040 2.00e-02 2.50e+03 pdb=" C4 C W 18 " -0.080 2.00e-02 2.50e+03 pdb=" N4 C W 18 " -0.326 2.00e-02 2.50e+03 pdb=" C5 C W 18 " 0.077 2.00e-02 2.50e+03 pdb=" C6 C W 18 " 0.112 2.00e-02 2.50e+03 pdb=" H5 C W 18 " 0.150 2.00e-02 2.50e+03 pdb=" H6 C W 18 " 0.184 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G W 19 " 0.534 2.00e-02 2.50e+03 1.90e-01 1.27e+03 pdb=" N9 G W 19 " -0.046 2.00e-02 2.50e+03 pdb=" C8 G W 19 " -0.134 2.00e-02 2.50e+03 pdb=" N7 G W 19 " -0.151 2.00e-02 2.50e+03 pdb=" C5 G W 19 " -0.058 2.00e-02 2.50e+03 pdb=" C6 G W 19 " 0.098 2.00e-02 2.50e+03 pdb=" O6 G W 19 " 0.306 2.00e-02 2.50e+03 pdb=" N1 G W 19 " 0.007 2.00e-02 2.50e+03 pdb=" C2 G W 19 " -0.067 2.00e-02 2.50e+03 pdb=" N2 G W 19 " -0.109 2.00e-02 2.50e+03 pdb=" N3 G W 19 " -0.145 2.00e-02 2.50e+03 pdb=" C4 G W 19 " -0.119 2.00e-02 2.50e+03 pdb=" H8 G W 19 " -0.142 2.00e-02 2.50e+03 pdb=" H1 G W 19 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U W 30 " 0.482 2.00e-02 2.50e+03 1.90e-01 1.08e+03 pdb=" N1 U W 30 " -0.042 2.00e-02 2.50e+03 pdb=" C2 U W 30 " -0.134 2.00e-02 2.50e+03 pdb=" O2 U W 30 " -0.182 2.00e-02 2.50e+03 pdb=" N3 U W 30 " -0.102 2.00e-02 2.50e+03 pdb=" C4 U W 30 " 0.064 2.00e-02 2.50e+03 pdb=" O4 U W 30 " 0.302 2.00e-02 2.50e+03 pdb=" C5 U W 30 " -0.055 2.00e-02 2.50e+03 pdb=" C6 U W 30 " -0.118 2.00e-02 2.50e+03 pdb=" H5 U W 30 " -0.056 2.00e-02 2.50e+03 pdb=" H3 U W 30 " -0.013 2.00e-02 2.50e+03 pdb=" H6 U W 30 " -0.145 2.00e-02 2.50e+03 ... (remaining 2260 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 522 2.01 - 2.65: 19700 2.65 - 3.30: 51926 3.30 - 3.95: 67667 3.95 - 4.60: 100314 Nonbonded interactions: 240129 Sorted by model distance: nonbonded pdb=" OH TYR P 225 " pdb=" O2 DT T 0 " model vdw 1.358 2.800 nonbonded pdb="HO2' A W 16 " pdb=" OP1 U W 17 " model vdw 1.560 2.450 nonbonded pdb="HO2' U W 30 " pdb=" OP1 U W 31 " model vdw 1.566 2.450 nonbonded pdb="HO2' A W 7 " pdb=" OP1 C W 8 " model vdw 1.568 2.450 nonbonded pdb=" HG1 THR P 499 " pdb=" OE1 GLU P 506 " model vdw 1.569 2.450 ... (remaining 240124 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 group one per residue 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: 1.860 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: 0.100 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.830 Find NCS groups from input model: 0.060 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6084 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 : 0.013 0.052 9302 Z= 0.982 Angle : 1.855 14.246 12894 Z= 1.609 Chirality : 0.096 0.469 1434 Planarity : 0.024 0.245 1352 Dihedral : 20.920 177.192 3882 Min Nonbonded Distance : 1.358 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.01 % Favored : 93.54 % Rotamer: Outliers : 0.76 % Allowed : 3.28 % Favored : 95.96 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % 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: -1.31 (0.26), residues: 882 helix: -0.72 (0.22), residues: 402 sheet: -0.90 (0.55), residues: 67 loop : -0.86 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 53 TYR 0.148 0.020 TYR P 146 PHE 0.061 0.014 PHE B 111 TRP 0.100 0.029 TRP P 724 HIS 0.012 0.003 HIS P 667 Details of bonding type rmsd/Z covalent geometry : bond 0.01265 / 0.98 ( 9302) covalent geometry : angle 1.85491 / 1.61 (12894) hydrogen bonds : bond 0.14812 / 9.68 ( 436) hydrogen bonds : angle 7.41978 / 5.23 ( 1167) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 197 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 191 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 523 ARG cc_start: 0.7826 (ttp-170) cc_final: 0.7588 (ttt180) REVERT: P 535 ARG cc_start: 0.8051 (ptm160) cc_final: 0.7297 (ptt90) outliers start: 6 outliers final: 2 residues processed: 194 average time/residue: 0.3021 time to fit residues: 74.5136 Evaluate side-chains 115 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 810 GLU Chi-restraints excluded: chain P residue 814 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 595 GLN P 665 GLN P 825 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.119866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.094266 restraints weight = 68760.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.098275 restraints weight = 29307.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.100679 restraints weight = 18099.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.102149 restraints weight = 13863.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.103069 restraints weight = 11821.677| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9302 Z= 0.208 Angle : 0.895 9.992 12894 Z= 0.506 Chirality : 0.055 0.326 1434 Planarity : 0.007 0.092 1352 Dihedral : 24.362 175.136 2031 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.97 % Favored : 95.92 % Rotamer: Outliers : 1.64 % Allowed : 9.22 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.26), residues: 882 helix: 0.14 (0.24), residues: 406 sheet: -0.93 (0.49), residues: 91 loop : -1.23 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 193 TYR 0.025 0.002 TYR P 349 PHE 0.022 0.002 PHE P 168 TRP 0.018 0.002 TRP P 724 HIS 0.007 0.002 HIS P 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.21 ( 9302) covalent geometry : angle 0.89461 / 0.51 (12894) hydrogen bonds : bond 0.06891 / 4.85 ( 436) hydrogen bonds : angle 5.49150 / 3.97 ( 1167) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8076 (ttp80) cc_final: 0.7825 (ttp80) REVERT: P 256 LYS cc_start: 0.8238 (tttt) cc_final: 0.8018 (ttmm) REVERT: P 301 MET cc_start: 0.8005 (mmm) cc_final: 0.7685 (mmm) REVERT: P 535 ARG cc_start: 0.8129 (ptm160) cc_final: 0.7433 (ptt90) REVERT: P 575 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6620 (mt-10) REVERT: P 772 LYS cc_start: 0.7842 (mmtt) cc_final: 0.7596 (mmtt) outliers start: 13 outliers final: 13 residues processed: 125 average time/residue: 0.3210 time to fit residues: 51.2435 Evaluate side-chains 103 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain P residue 108 ILE Chi-restraints excluded: chain P residue 250 ILE Chi-restraints excluded: chain P residue 410 LEU Chi-restraints excluded: chain P residue 507 ILE Chi-restraints excluded: chain P residue 627 SER Chi-restraints excluded: chain P residue 675 ILE Chi-restraints excluded: chain P residue 709 ILE Chi-restraints excluded: chain P residue 753 LEU Chi-restraints excluded: chain P residue 783 ASN Chi-restraints excluded: chain P residue 810 GLU Chi-restraints excluded: chain P residue 814 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 9 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 603 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.117967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.091979 restraints weight = 69503.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.095857 restraints weight = 29925.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.098267 restraints weight = 18776.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.099660 restraints weight = 14366.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.100478 restraints weight = 12341.561| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9302 Z= 0.225 Angle : 0.772 8.877 12894 Z= 0.445 Chirality : 0.050 0.294 1434 Planarity : 0.006 0.082 1352 Dihedral : 24.146 170.180 2031 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.67 % Favored : 94.22 % Rotamer: Outliers : 1.89 % Allowed : 10.61 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.27), residues: 882 helix: 0.35 (0.24), residues: 406 sheet: -1.05 (0.47), residues: 91 loop : -1.36 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 758 TYR 0.015 0.002 TYR P 205 PHE 0.024 0.002 PHE P 158 TRP 0.013 0.002 TRP P 724 HIS 0.008 0.001 HIS P 671 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.22 ( 9302) covalent geometry : angle 0.77179 / 0.44 (12894) hydrogen bonds : bond 0.05844 / 3.99 ( 436) hydrogen bonds : angle 5.28426 / 3.85 ( 1167) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 256 LYS cc_start: 0.8243 (tttt) cc_final: 0.8012 (ttmm) REVERT: P 301 MET cc_start: 0.8081 (mmm) cc_final: 0.7719 (mmm) REVERT: P 494 TYR cc_start: 0.8043 (t80) cc_final: 0.7728 (t80) REVERT: P 523 ARG cc_start: 0.7935 (ttp-170) cc_final: 0.7149 (ttm170) REVERT: P 575 GLU cc_start: 0.7396 (mt-10) cc_final: 0.6781 (mt-10) REVERT: P 685 LEU cc_start: 0.8921 (mt) cc_final: 0.8677 (mp) outliers start: 15 outliers final: 11 residues processed: 100 average time/residue: 0.2794 time to fit residues: 36.6819 Evaluate side-chains 93 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain P residue 108 ILE Chi-restraints excluded: chain P residue 410 LEU Chi-restraints excluded: chain P residue 448 ARG Chi-restraints excluded: chain P residue 590 ASP Chi-restraints excluded: chain P residue 675 ILE Chi-restraints excluded: chain P residue 709 ILE Chi-restraints excluded: chain P residue 753 LEU Chi-restraints excluded: chain P residue 783 ASN Chi-restraints excluded: chain P residue 810 GLU Chi-restraints excluded: chain P residue 814 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 16 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 64 optimal weight: 0.3980 chunk 1 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 52 HIS P 300 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.118750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.092659 restraints weight = 68514.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.096610 restraints weight = 29726.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.099013 restraints weight = 18587.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.100371 restraints weight = 14222.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.101276 restraints weight = 12243.765| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9302 Z= 0.177 Angle : 0.706 9.443 12894 Z= 0.402 Chirality : 0.046 0.294 1434 Planarity : 0.005 0.062 1352 Dihedral : 24.015 176.375 2031 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.54 % Favored : 95.35 % Rotamer: Outliers : 1.89 % Allowed : 10.98 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.72 (0.27), residues: 882 helix: 0.65 (0.25), residues: 405 sheet: -1.20 (0.46), residues: 92 loop : -1.50 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 652 TYR 0.015 0.002 TYR P 205 PHE 0.023 0.002 PHE P 158 TRP 0.012 0.001 TRP P 724 HIS 0.003 0.001 HIS P 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.18 ( 9302) covalent geometry : angle 0.70553 / 0.40 (12894) hydrogen bonds : bond 0.05152 / 3.53 ( 436) hydrogen bonds : angle 5.04475 / 3.68 ( 1167) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 301 MET cc_start: 0.8048 (mmm) cc_final: 0.7700 (mmm) REVERT: P 494 TYR cc_start: 0.7704 (t80) cc_final: 0.7445 (t80) REVERT: P 523 ARG cc_start: 0.7930 (ttp-170) cc_final: 0.7132 (ttm170) REVERT: P 575 GLU cc_start: 0.7389 (mt-10) cc_final: 0.6751 (mt-10) REVERT: P 597 CYS cc_start: 0.6401 (m) cc_final: 0.6102 (m) REVERT: P 756 GLU cc_start: 0.5828 (OUTLIER) cc_final: 0.5091 (pt0) outliers start: 15 outliers final: 8 residues processed: 103 average time/residue: 0.2585 time to fit residues: 35.5068 Evaluate side-chains 86 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain P residue 108 ILE Chi-restraints excluded: chain P residue 590 ASP Chi-restraints excluded: chain P residue 675 ILE Chi-restraints excluded: chain P residue 709 ILE Chi-restraints excluded: chain P residue 756 GLU Chi-restraints excluded: chain P residue 783 ASN Chi-restraints excluded: chain P residue 790 VAL Chi-restraints excluded: chain P residue 810 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 6 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 85 optimal weight: 0.0670 chunk 48 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 overall best weight: 1.3724 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.118697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.092922 restraints weight = 67044.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.096793 restraints weight = 28763.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.099106 restraints weight = 17901.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.100609 restraints weight = 13717.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.101324 restraints weight = 11650.348| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9302 Z= 0.155 Angle : 0.661 9.032 12894 Z= 0.380 Chirality : 0.045 0.272 1434 Planarity : 0.005 0.084 1352 Dihedral : 23.835 176.121 2027 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.65 % Favored : 95.24 % Rotamer: Outliers : 1.26 % Allowed : 12.25 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.55 (0.27), residues: 882 helix: 0.79 (0.25), residues: 410 sheet: -1.28 (0.47), residues: 90 loop : -1.39 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 652 TYR 0.021 0.002 TYR P 386 PHE 0.020 0.001 PHE P 158 TRP 0.011 0.001 TRP P 724 HIS 0.003 0.001 HIS P 671 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 ( 9302) covalent geometry : angle 0.66137 / 0.38 (12894) hydrogen bonds : bond 0.04868 / 3.29 ( 436) hydrogen bonds : angle 4.90074 / 3.55 ( 1167) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 301 MET cc_start: 0.8086 (mmm) cc_final: 0.7690 (mmm) REVERT: P 494 TYR cc_start: 0.7841 (t80) cc_final: 0.7520 (t80) REVERT: P 513 ASN cc_start: 0.8073 (p0) cc_final: 0.7873 (p0) REVERT: P 523 ARG cc_start: 0.7954 (ttp-170) cc_final: 0.7160 (ttm170) REVERT: P 575 GLU cc_start: 0.7407 (mt-10) cc_final: 0.6735 (mt-10) REVERT: P 756 GLU cc_start: 0.5850 (OUTLIER) cc_final: 0.5070 (pt0) outliers start: 10 outliers final: 7 residues processed: 88 average time/residue: 0.2482 time to fit residues: 29.6038 Evaluate side-chains 87 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain P residue 108 ILE Chi-restraints excluded: chain P residue 410 LEU Chi-restraints excluded: chain P residue 448 ARG Chi-restraints excluded: chain P residue 709 ILE Chi-restraints excluded: chain P residue 756 GLU Chi-restraints excluded: chain P residue 790 VAL Chi-restraints excluded: chain P residue 810 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 63 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.117934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.092113 restraints weight = 66871.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.095919 restraints weight = 29004.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.098239 restraints weight = 18185.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.099670 restraints weight = 13949.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.100367 restraints weight = 11942.819| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9302 Z= 0.187 Angle : 0.661 9.104 12894 Z= 0.379 Chirality : 0.045 0.250 1434 Planarity : 0.005 0.054 1352 Dihedral : 23.675 173.659 2027 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.90 % Favored : 93.99 % Rotamer: Outliers : 1.52 % Allowed : 12.37 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.57 (0.27), residues: 882 helix: 0.87 (0.25), residues: 410 sheet: -1.37 (0.47), residues: 90 loop : -1.51 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 758 TYR 0.019 0.002 TYR P 218 PHE 0.024 0.002 PHE P 158 TRP 0.012 0.001 TRP P 724 HIS 0.003 0.001 HIS P 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.19 ( 9302) covalent geometry : angle 0.66148 / 0.38 (12894) hydrogen bonds : bond 0.05030 / 3.39 ( 436) hydrogen bonds : angle 4.89214 / 3.55 ( 1167) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 95 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 301 MET cc_start: 0.8126 (mmm) cc_final: 0.7730 (mmm) REVERT: P 494 TYR cc_start: 0.7877 (t80) cc_final: 0.7522 (t80) REVERT: P 575 GLU cc_start: 0.7464 (mt-10) cc_final: 0.6802 (mt-10) REVERT: P 756 GLU cc_start: 0.5859 (OUTLIER) cc_final: 0.5154 (pt0) outliers start: 12 outliers final: 7 residues processed: 89 average time/residue: 0.2268 time to fit residues: 27.1473 Evaluate side-chains 86 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain P residue 108 ILE Chi-restraints excluded: chain P residue 448 ARG Chi-restraints excluded: chain P residue 590 ASP Chi-restraints excluded: chain P residue 709 ILE Chi-restraints excluded: chain P residue 756 GLU Chi-restraints excluded: chain P residue 776 ILE Chi-restraints excluded: chain P residue 790 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 87 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 385 ASN ** 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 = 0.4119 r_free = 0.4119 target = 0.118486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.092709 restraints weight = 67035.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.096498 restraints weight = 28909.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.098890 restraints weight = 18063.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.100326 restraints weight = 13744.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.101120 restraints weight = 11718.131| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9302 Z= 0.147 Angle : 0.626 8.814 12894 Z= 0.359 Chirality : 0.044 0.277 1434 Planarity : 0.005 0.072 1352 Dihedral : 23.561 174.644 2024 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.42 % Favored : 95.35 % Rotamer: Outliers : 1.14 % Allowed : 12.63 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.43 (0.27), residues: 882 helix: 1.04 (0.25), residues: 409 sheet: -1.39 (0.46), residues: 90 loop : -1.48 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 448 TYR 0.012 0.001 TYR P 205 PHE 0.018 0.001 PHE P 158 TRP 0.011 0.001 TRP P 724 HIS 0.003 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 ( 9302) covalent geometry : angle 0.62576 / 0.36 (12894) hydrogen bonds : bond 0.04664 / 3.11 ( 436) hydrogen bonds : angle 4.81109 / 3.54 ( 1167) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 LEU cc_start: 0.7720 (mt) cc_final: 0.7482 (tp) REVERT: P 301 MET cc_start: 0.8126 (mmm) cc_final: 0.7763 (mmm) REVERT: P 494 TYR cc_start: 0.7867 (t80) cc_final: 0.7458 (t80) REVERT: P 575 GLU cc_start: 0.7474 (mt-10) cc_final: 0.6801 (mt-10) REVERT: P 756 GLU cc_start: 0.5717 (OUTLIER) cc_final: 0.4993 (pt0) outliers start: 9 outliers final: 6 residues processed: 86 average time/residue: 0.2474 time to fit residues: 28.3996 Evaluate side-chains 85 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain P residue 108 ILE Chi-restraints excluded: chain P residue 590 ASP Chi-restraints excluded: chain P residue 709 ILE Chi-restraints excluded: chain P residue 756 GLU Chi-restraints excluded: chain P residue 776 ILE Chi-restraints excluded: chain P residue 790 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 84 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 385 ASN ** 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 = 0.4081 r_free = 0.4081 target = 0.116026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.090104 restraints weight = 68151.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.093778 restraints weight = 30036.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.096057 restraints weight = 18993.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.097397 restraints weight = 14603.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.098261 restraints weight = 12565.483| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9302 Z= 0.276 Angle : 0.701 8.932 12894 Z= 0.400 Chirality : 0.046 0.281 1434 Planarity : 0.005 0.072 1352 Dihedral : 23.543 174.703 2024 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.12 % Favored : 93.65 % Rotamer: Outliers : 1.39 % Allowed : 13.26 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.79 (0.27), residues: 882 helix: 0.85 (0.25), residues: 402 sheet: -1.59 (0.46), residues: 92 loop : -1.74 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 610 TYR 0.015 0.002 TYR P 601 PHE 0.029 0.002 PHE P 158 TRP 0.012 0.001 TRP P 724 HIS 0.006 0.002 HIS P 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.28 ( 9302) covalent geometry : angle 0.70061 / 0.40 (12894) hydrogen bonds : bond 0.05718 / 3.83 ( 436) hydrogen bonds : angle 5.00782 / 3.63 ( 1167) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 LEU cc_start: 0.7779 (mt) cc_final: 0.7573 (tp) REVERT: P 301 MET cc_start: 0.8124 (mmm) cc_final: 0.7715 (mmm) REVERT: P 494 TYR cc_start: 0.8038 (t80) cc_final: 0.7627 (t80) REVERT: P 575 GLU cc_start: 0.7559 (mt-10) cc_final: 0.6894 (mt-10) REVERT: P 756 GLU cc_start: 0.5770 (OUTLIER) cc_final: 0.5248 (pt0) outliers start: 11 outliers final: 7 residues processed: 84 average time/residue: 0.2174 time to fit residues: 25.0287 Evaluate side-chains 82 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain P residue 108 ILE Chi-restraints excluded: chain P residue 448 ARG Chi-restraints excluded: chain P residue 590 ASP Chi-restraints excluded: chain P residue 709 ILE Chi-restraints excluded: chain P residue 756 GLU Chi-restraints excluded: chain P residue 776 ILE Chi-restraints excluded: chain P residue 790 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 38 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.4085 r_free = 0.4085 target = 0.116390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.090259 restraints weight = 68833.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.094040 restraints weight = 30503.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.096374 restraints weight = 19270.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.097742 restraints weight = 14841.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.098551 restraints weight = 12796.403| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.5371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9302 Z= 0.204 Angle : 0.653 8.789 12894 Z= 0.375 Chirality : 0.044 0.260 1434 Planarity : 0.005 0.067 1352 Dihedral : 23.562 174.463 2024 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.67 % Favored : 94.10 % Rotamer: Outliers : 1.39 % Allowed : 13.76 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.78 (0.27), residues: 882 helix: 0.85 (0.25), residues: 404 sheet: -1.67 (0.47), residues: 90 loop : -1.72 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 652 TYR 0.013 0.002 TYR P 205 PHE 0.026 0.002 PHE P 318 TRP 0.011 0.001 TRP P 724 HIS 0.003 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.20 ( 9302) covalent geometry : angle 0.65308 / 0.38 (12894) hydrogen bonds : bond 0.05241 / 3.48 ( 436) hydrogen bonds : angle 4.94355 / 3.64 ( 1167) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 87 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 301 MET cc_start: 0.8132 (mmm) cc_final: 0.7724 (mmm) REVERT: P 494 TYR cc_start: 0.8012 (t80) cc_final: 0.7622 (t80) REVERT: P 575 GLU cc_start: 0.7540 (mt-10) cc_final: 0.6863 (mt-10) REVERT: P 756 GLU cc_start: 0.5760 (OUTLIER) cc_final: 0.5252 (pt0) outliers start: 11 outliers final: 8 residues processed: 83 average time/residue: 0.2390 time to fit residues: 26.9416 Evaluate side-chains 84 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain P residue 108 ILE Chi-restraints excluded: chain P residue 590 ASP Chi-restraints excluded: chain P residue 709 ILE Chi-restraints excluded: chain P residue 719 LEU Chi-restraints excluded: chain P residue 756 GLU Chi-restraints excluded: chain P residue 776 ILE Chi-restraints excluded: chain P residue 790 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 79 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.117094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.091317 restraints weight = 67080.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.095071 restraints weight = 29163.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.097393 restraints weight = 18277.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.098752 restraints weight = 14011.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.099500 restraints weight = 12046.433| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9302 Z= 0.161 Angle : 0.631 8.379 12894 Z= 0.361 Chirality : 0.044 0.265 1434 Planarity : 0.005 0.061 1352 Dihedral : 23.567 175.199 2024 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.78 % Favored : 93.99 % Rotamer: Outliers : 1.14 % Allowed : 14.14 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.27), residues: 882 helix: 1.01 (0.25), residues: 404 sheet: -1.66 (0.48), residues: 90 loop : -1.62 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 53 TYR 0.029 0.002 TYR B 46 PHE 0.024 0.002 PHE P 318 TRP 0.012 0.001 TRP P 724 HIS 0.004 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 ( 9302) covalent geometry : angle 0.63148 / 0.36 (12894) hydrogen bonds : bond 0.04889 / 3.25 ( 436) hydrogen bonds : angle 4.83966 / 3.53 ( 1167) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 180 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Evaluate side-chains 88 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 301 MET cc_start: 0.8148 (mmm) cc_final: 0.7754 (mmm) REVERT: P 494 TYR cc_start: 0.7905 (t80) cc_final: 0.7461 (t80) REVERT: P 575 GLU cc_start: 0.7484 (mt-10) cc_final: 0.6773 (mt-10) REVERT: P 756 GLU cc_start: 0.5715 (OUTLIER) cc_final: 0.5196 (pt0) outliers start: 9 outliers final: 8 residues processed: 84 average time/residue: 0.2106 time to fit residues: 23.9814 Evaluate side-chains 83 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain P residue 108 ILE Chi-restraints excluded: chain P residue 448 ARG Chi-restraints excluded: chain P residue 590 ASP Chi-restraints excluded: chain P residue 709 ILE Chi-restraints excluded: chain P residue 719 LEU Chi-restraints excluded: chain P residue 756 GLU Chi-restraints excluded: chain P residue 776 ILE Chi-restraints excluded: chain P residue 790 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 72 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.117803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.092164 restraints weight = 67190.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.095933 restraints weight = 28926.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.098331 restraints weight = 18027.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.099684 restraints weight = 13715.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.100447 restraints weight = 11781.748| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9302 Z= 0.147 Angle : 0.615 8.601 12894 Z= 0.351 Chirality : 0.042 0.278 1434 Planarity : 0.005 0.057 1352 Dihedral : 23.581 175.784 2024 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.44 % Favored : 94.44 % Rotamer: Outliers : 1.26 % Allowed : 14.02 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.46 (0.27), residues: 882 helix: 1.17 (0.25), residues: 404 sheet: -1.61 (0.49), residues: 90 loop : -1.59 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 839 TYR 0.018 0.001 TYR B 46 PHE 0.024 0.002 PHE P 318 TRP 0.013 0.001 TRP P 724 HIS 0.004 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 ( 9302) covalent geometry : angle 0.61514 / 0.35 (12894) hydrogen bonds : bond 0.04698 / 3.08 ( 436) hydrogen bonds : angle 4.77579 / 3.49 ( 1167) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3019.46 seconds wall clock time: 52 minutes 17.23 seconds (3137.23 seconds total)