Starting phenix.real_space_refine on Thu Sep 18 13:03:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cf1_45526/09_2025/9cf1_45526_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cf1_45526/09_2025/9cf1_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 { model { file = "/net/cci-nas-00/data/ceres_data/9cf1_45526/09_2025/9cf1_45526_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cf1_45526/09_2025/9cf1_45526_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cf1_45526/09_2025/9cf1_45526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cf1_45526/09_2025/9cf1_45526.map" } 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-2.0-5805/lib/python3.9/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: 3.15, per 1000 atoms: 0.18 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: 1.78 Conformation dependent library (CDL) restraints added in 450.4 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 2.72 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: 4.22 Time building geometry restraints manager: 2.34 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: 27772 2.85 - 5.70: 3120 5.70 - 8.55: 716 8.55 - 11.40: 20 11.40 - 14.25: 14 Bond angle restraints: 31642 Sorted by residual: angle pdb=" O3' U W 31 " pdb=" C3' U W 31 " pdb=" C2' U W 31 " ideal model delta sigma weight residual 109.50 123.75 -14.25 1.50e+00 4.44e-01 9.02e+01 angle pdb=" O3' U W 30 " pdb=" C3' U W 30 " pdb=" C2' U W 30 " ideal model delta sigma weight residual 109.50 121.78 -12.28 1.50e+00 4.44e-01 6.71e+01 angle pdb=" CA PHE P 826 " pdb=" CB PHE P 826 " pdb=" CG PHE P 826 " ideal model delta sigma weight residual 113.80 121.87 -8.07 1.00e+00 1.00e+00 6.51e+01 angle pdb=" CA ASP P 769 " pdb=" CB ASP P 769 " pdb=" CG ASP P 769 " ideal model delta sigma weight residual 112.60 120.06 -7.46 1.00e+00 1.00e+00 5.56e+01 angle pdb=" CA PRO P 103 " pdb=" N PRO P 103 " pdb=" CD PRO P 103 " ideal model delta sigma weight residual 112.00 102.24 9.76 1.40e+00 5.10e-01 4.86e+01 ... (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: 345 0.188 - 0.281: 63 0.281 - 0.375: 11 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' 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 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 -2.66 -2.27 -0.39 2.00e-01 2.50e+01 3.82e+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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.480 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5947 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= 0.727 Angle : 1.844 14.246 12894 Z= 1.225 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 aren 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 covalent geometry : bond 0.01259 ( 9302) covalent geometry : angle 1.84432 (12894) hydrogen bonds : bond 0.14812 ( 436) hydrogen bonds : angle 7.41978 ( 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 : 0.435 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: 0.7548 (ttt180) REVERT: P 535 ARG cc_start: 0.8051 (ptm160) cc_final: 0.7306 (ptt90) outliers start: 6 outliers final: 2 residues processed: 194 average time/residue: 0.3331 time to fit residues: 80.4590 Evaluate side-chains 113 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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: 0.9980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4157 r_free = 0.4157 target = 0.120872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.095303 restraints weight = 68574.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.099285 restraints weight = 29343.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.101661 restraints weight = 18225.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.103155 restraints weight = 13971.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.103907 restraints weight = 11910.173| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9302 Z= 0.184 Angle : 0.760 8.144 12894 Z= 0.421 Chirality : 0.045 0.227 1434 Planarity : 0.005 0.057 1352 Dihedral : 24.114 171.371 2031 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.08 % Favored : 95.80 % Rotamer: Outliers : 0.88 % Allowed : 9.09 % Favored : 90.03 % 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 aren not related in a simple way. whole: -0.27 (0.27), residues: 882 helix: 0.85 (0.24), residues: 404 sheet: -0.94 (0.47), residues: 91 loop : -1.05 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 489 TYR 0.022 0.002 TYR P 349 PHE 0.026 0.002 PHE P 143 TRP 0.012 0.002 TRP P 816 HIS 0.004 0.001 HIS P 671 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 9302) covalent geometry : angle 0.76016 (12894) hydrogen bonds : bond 0.05136 ( 436) hydrogen bonds : angle 5.12265 ( 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 126 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.285 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: P 256 LYS cc_start: 0.8194 (tttt) cc_final: 0.7974 (ttmm) REVERT: P 301 MET cc_start: 0.8015 (mmm) cc_final: 0.7701 (mmm) REVERT: P 505 LYS cc_start: 0.6931 (mttt) cc_final: 0.6530 (mmtt) REVERT: P 523 ARG cc_start: 0.7903 (ttp-170) cc_final: 0.7082 (mtm-85) REVERT: P 575 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6653 (mt-10) outliers start: 7 outliers final: 5 residues processed: 122 average time/residue: 0.2794 time to fit residues: 43.0199 Evaluate side-chains 101 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 108 ILE Chi-restraints excluded: chain P residue 410 LEU Chi-restraints excluded: chain P residue 675 ILE Chi-restraints excluded: chain P residue 709 ILE 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: 0.7980 chunk 35 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 78 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.121495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.095557 restraints weight = 69080.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.099663 restraints weight = 29802.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.102112 restraints weight = 18498.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.103634 restraints weight = 14131.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.104374 restraints weight = 12037.618| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9302 Z= 0.143 Angle : 0.636 7.393 12894 Z= 0.357 Chirality : 0.041 0.177 1434 Planarity : 0.004 0.045 1352 Dihedral : 23.619 176.095 2028 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.63 % Favored : 96.26 % Rotamer: Outliers : 1.52 % Allowed : 9.47 % Favored : 89.02 % 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 aren not related in a simple way. whole: 0.13 (0.27), residues: 882 helix: 1.43 (0.25), residues: 400 sheet: -1.14 (0.45), residues: 92 loop : -1.01 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 193 TYR 0.013 0.001 TYR P 600 PHE 0.023 0.002 PHE B 34 TRP 0.013 0.001 TRP P 724 HIS 0.007 0.001 HIS P 671 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9302) covalent geometry : angle 0.63603 (12894) hydrogen bonds : bond 0.04385 ( 436) hydrogen bonds : angle 4.73720 ( 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 118 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.394 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 256 LYS cc_start: 0.8197 (tttt) cc_final: 0.7968 (ttmm) REVERT: P 301 MET cc_start: 0.8064 (mmm) cc_final: 0.7733 (mmm) REVERT: P 483 VAL cc_start: 0.8956 (t) cc_final: 0.8713 (p) REVERT: P 494 TYR cc_start: 0.7792 (t80) cc_final: 0.7523 (t80) REVERT: P 523 ARG cc_start: 0.7914 (ttp-170) cc_final: 0.7085 (mtm-85) REVERT: P 575 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6529 (mt-10) outliers start: 12 outliers final: 4 residues processed: 114 average time/residue: 0.2784 time to fit residues: 40.7421 Evaluate side-chains 95 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain P residue 709 ILE Chi-restraints excluded: chain P residue 790 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 16 optimal weight: 6.9990 chunk 86 optimal weight: 0.0770 chunk 7 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 HIS ** P 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 603 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.119565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.093474 restraints weight = 68244.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.097375 restraints weight = 29931.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.099777 restraints weight = 18802.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.101250 restraints weight = 14418.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.101973 restraints weight = 12348.583| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9302 Z= 0.163 Angle : 0.621 7.003 12894 Z= 0.347 Chirality : 0.040 0.182 1434 Planarity : 0.005 0.067 1352 Dihedral : 23.345 177.214 2024 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.54 % Favored : 95.35 % Rotamer: Outliers : 1.39 % Allowed : 9.47 % Favored : 89.14 % 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 aren not related in a simple way. whole: 0.24 (0.28), residues: 882 helix: 1.51 (0.25), residues: 409 sheet: -1.29 (0.45), residues: 90 loop : -0.94 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 814 TYR 0.011 0.001 TYR P 205 PHE 0.018 0.001 PHE P 158 TRP 0.011 0.001 TRP P 724 HIS 0.002 0.001 HIS P 241 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 9302) covalent geometry : angle 0.62139 (12894) hydrogen bonds : bond 0.04504 ( 436) hydrogen bonds : angle 4.63439 ( 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 109 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.428 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 256 LYS cc_start: 0.8155 (tttt) cc_final: 0.7856 (ttmm) REVERT: P 301 MET cc_start: 0.8177 (mmm) cc_final: 0.7751 (mmm) REVERT: P 494 TYR cc_start: 0.7888 (t80) cc_final: 0.7409 (t80) REVERT: P 523 ARG cc_start: 0.8002 (ttp-170) cc_final: 0.7191 (mtm-85) REVERT: P 575 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6447 (mt-10) outliers start: 11 outliers final: 9 residues processed: 103 average time/residue: 0.2478 time to fit residues: 33.7157 Evaluate side-chains 93 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 397 MET 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 776 ILE Chi-restraints excluded: chain P residue 790 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 6 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.119250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.093309 restraints weight = 67039.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.097126 restraints weight = 29096.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.099429 restraints weight = 18249.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.100901 restraints weight = 14036.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.101731 restraints weight = 11998.345| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9302 Z= 0.152 Angle : 0.604 10.095 12894 Z= 0.336 Chirality : 0.040 0.177 1434 Planarity : 0.004 0.059 1352 Dihedral : 23.274 176.767 2024 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.20 % Favored : 95.69 % Rotamer: Outliers : 1.64 % Allowed : 9.85 % Favored : 88.51 % 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 aren not related in a simple way. whole: 0.36 (0.28), residues: 882 helix: 1.63 (0.25), residues: 410 sheet: -1.30 (0.45), residues: 90 loop : -0.90 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 448 TYR 0.010 0.001 TYR P 600 PHE 0.024 0.001 PHE P 348 TRP 0.011 0.001 TRP P 724 HIS 0.003 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9302) covalent geometry : angle 0.60402 (12894) hydrogen bonds : bond 0.04289 ( 436) hydrogen bonds : angle 4.59106 ( 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 98 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.453 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: P 256 LYS cc_start: 0.8136 (tttt) cc_final: 0.7834 (ttmm) REVERT: P 301 MET cc_start: 0.8183 (mmm) cc_final: 0.7764 (mmm) REVERT: P 494 TYR cc_start: 0.7682 (t80) cc_final: 0.7286 (t80) REVERT: P 523 ARG cc_start: 0.7993 (ttp-170) cc_final: 0.7181 (mtm-85) REVERT: P 575 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6444 (mt-10) REVERT: P 756 GLU cc_start: 0.5394 (OUTLIER) cc_final: 0.5114 (pt0) outliers start: 13 outliers final: 10 residues processed: 91 average time/residue: 0.2414 time to fit residues: 29.2100 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 : 0.427 ------------------------------------------------------------------------------- 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 397 MET Chi-restraints excluded: chain P residue 448 ARG Chi-restraints excluded: chain P residue 467 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 63 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.118594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.092366 restraints weight = 68081.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.096151 restraints weight = 29877.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.098522 restraints weight = 18894.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.099854 restraints weight = 14529.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.100662 restraints weight = 12539.883| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.5739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9302 Z= 0.167 Angle : 0.599 7.341 12894 Z= 0.332 Chirality : 0.040 0.187 1434 Planarity : 0.005 0.061 1352 Dihedral : 23.245 178.163 2024 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.54 % Favored : 95.35 % Rotamer: Outliers : 1.89 % Allowed : 10.10 % Favored : 88.01 % 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 aren not related in a simple way. whole: 0.36 (0.28), residues: 882 helix: 1.72 (0.25), residues: 410 sheet: -1.36 (0.45), residues: 90 loop : -0.99 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 448 TYR 0.012 0.001 TYR P 601 PHE 0.018 0.002 PHE P 158 TRP 0.011 0.001 TRP P 724 HIS 0.003 0.001 HIS P 241 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 9302) covalent geometry : angle 0.59867 (12894) hydrogen bonds : bond 0.04483 ( 436) hydrogen bonds : angle 4.59906 ( 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 98 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.374 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: 0.8163 (mmm) cc_final: 0.7729 (mmm) REVERT: P 575 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6580 (mt-10) outliers start: 15 outliers final: 11 residues processed: 93 average time/residue: 0.2243 time to fit residues: 27.6560 Evaluate side-chains 86 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 397 MET Chi-restraints excluded: chain P residue 448 ARG Chi-restraints excluded: chain P residue 492 LEU Chi-restraints excluded: chain P residue 590 ASP Chi-restraints excluded: chain P residue 644 SER Chi-restraints excluded: chain P residue 709 ILE Chi-restraints excluded: chain P residue 719 LEU 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: 1.9990 chunk 11 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.117762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.091809 restraints weight = 67028.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.095559 restraints weight = 29381.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.097877 restraints weight = 18485.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.099254 restraints weight = 14171.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.100059 restraints weight = 12148.674| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.5936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9302 Z= 0.183 Angle : 0.602 7.910 12894 Z= 0.334 Chirality : 0.040 0.218 1434 Planarity : 0.005 0.062 1352 Dihedral : 23.217 177.620 2024 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.76 % Favored : 95.12 % Rotamer: Outliers : 1.52 % Allowed : 11.36 % 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 aren not related in a simple way. whole: 0.21 (0.28), residues: 882 helix: 1.64 (0.25), residues: 410 sheet: -1.45 (0.46), residues: 90 loop : -1.13 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 448 TYR 0.017 0.001 TYR B 46 PHE 0.020 0.002 PHE P 318 TRP 0.010 0.001 TRP P 724 HIS 0.003 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9302) covalent geometry : angle 0.60180 (12894) hydrogen bonds : bond 0.04533 ( 436) hydrogen bonds : angle 4.60771 ( 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: 12 poor density : 77 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: P 301 MET cc_start: 0.8122 (mmm) cc_final: 0.7729 (mmm) REVERT: P 575 GLU cc_start: 0.7425 (mt-10) cc_final: 0.6699 (mt-10) outliers start: 12 outliers final: 10 residues processed: 83 average time/residue: 0.2349 time to fit residues: 26.4703 Evaluate side-chains 83 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 397 MET Chi-restraints excluded: chain P residue 448 ARG Chi-restraints excluded: chain P residue 492 LEU 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 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: 0.8980 chunk 95 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.118116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.092308 restraints weight = 67405.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.096058 restraints weight = 29518.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.098433 restraints weight = 18532.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.099784 restraints weight = 14121.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.100490 restraints weight = 12146.672| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 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 0.037 9302 Z= 0.164 Angle : 0.582 8.037 12894 Z= 0.322 Chirality : 0.039 0.181 1434 Planarity : 0.004 0.057 1352 Dihedral : 23.209 177.798 2024 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.76 % Favored : 95.12 % Rotamer: Outliers : 1.64 % Allowed : 11.49 % Favored : 86.87 % 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 aren not related in a simple way. whole: 0.29 (0.28), residues: 882 helix: 1.74 (0.25), residues: 409 sheet: -1.43 (0.46), residues: 90 loop : -1.12 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 652 TYR 0.011 0.001 TYR B 46 PHE 0.020 0.002 PHE P 318 TRP 0.011 0.001 TRP P 724 HIS 0.005 0.001 HIS P 241 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9302) covalent geometry : angle 0.58156 (12894) hydrogen bonds : bond 0.04340 ( 436) hydrogen bonds : angle 4.52241 ( 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 88 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.459 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: B 37 LEU cc_start: 0.7316 (tp) cc_final: 0.7002 (tt) REVERT: P 301 MET cc_start: 0.8125 (mmm) cc_final: 0.7749 (mmm) REVERT: P 521 HIS cc_start: 0.6371 (t70) cc_final: 0.6157 (t70) REVERT: P 575 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6659 (mt-10) outliers start: 13 outliers final: 9 residues processed: 84 average time/residue: 0.2390 time to fit residues: 27.2376 Evaluate side-chains 81 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain P residue 108 ILE Chi-restraints excluded: chain P residue 397 MET Chi-restraints excluded: chain P residue 492 LEU Chi-restraints excluded: chain P residue 590 ASP Chi-restraints excluded: chain P residue 709 ILE 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: 5.9990 chunk 41 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 27 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.117837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.092031 restraints weight = 67680.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.095745 restraints weight = 29727.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.098088 restraints weight = 18768.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.099417 restraints weight = 14357.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.100251 restraints weight = 12337.555| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.6295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9302 Z= 0.176 Angle : 0.593 8.133 12894 Z= 0.329 Chirality : 0.039 0.183 1434 Planarity : 0.005 0.056 1352 Dihedral : 23.160 176.731 2024 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.76 % Favored : 95.12 % Rotamer: Outliers : 1.52 % Allowed : 11.87 % Favored : 86.62 % 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 aren not related in a simple way. whole: 0.24 (0.28), residues: 882 helix: 1.70 (0.25), residues: 409 sheet: -1.44 (0.47), residues: 90 loop : -1.15 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 652 TYR 0.011 0.001 TYR B 46 PHE 0.020 0.002 PHE P 318 TRP 0.011 0.001 TRP P 724 HIS 0.003 0.001 HIS P 241 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 9302) covalent geometry : angle 0.59336 (12894) hydrogen bonds : bond 0.04501 ( 436) hydrogen bonds : angle 4.51858 ( 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: 12 poor density : 75 time to evaluate : 0.329 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: B 37 LEU cc_start: 0.7329 (tp) cc_final: 0.7016 (tt) REVERT: P 301 MET cc_start: 0.8119 (mmm) cc_final: 0.7757 (mmm) REVERT: P 521 HIS cc_start: 0.6400 (t70) cc_final: 0.6188 (t70) REVERT: P 575 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6684 (mt-10) REVERT: P 618 HIS cc_start: 0.6159 (OUTLIER) cc_final: 0.5747 (t-170) outliers start: 12 outliers final: 10 residues processed: 82 average time/residue: 0.1969 time to fit residues: 22.6547 Evaluate side-chains 82 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain P residue 108 ILE Chi-restraints excluded: chain P residue 397 MET Chi-restraints excluded: chain P residue 448 ARG Chi-restraints excluded: chain P residue 492 LEU Chi-restraints excluded: chain P residue 590 ASP Chi-restraints excluded: chain P residue 618 HIS Chi-restraints excluded: chain P residue 709 ILE 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: 0.8980 chunk 73 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.117307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.091391 restraints weight = 66534.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.095195 restraints weight = 28963.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.097604 restraints weight = 18056.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.099054 restraints weight = 13711.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.099884 restraints weight = 11641.881| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.6439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9302 Z= 0.148 Angle : 0.575 7.734 12894 Z= 0.317 Chirality : 0.038 0.196 1434 Planarity : 0.004 0.049 1352 Dihedral : 23.068 175.781 2024 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.65 % Favored : 95.24 % Rotamer: Outliers : 1.64 % Allowed : 11.87 % 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 aren not related in a simple way. whole: 0.42 (0.28), residues: 882 helix: 1.87 (0.25), residues: 409 sheet: -1.36 (0.47), residues: 90 loop : -1.08 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 153 TYR 0.010 0.001 TYR B 46 PHE 0.020 0.001 PHE P 318 TRP 0.014 0.001 TRP P 724 HIS 0.003 0.001 HIS P 241 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9302) covalent geometry : angle 0.57500 (12894) hydrogen bonds : bond 0.04181 ( 436) hydrogen bonds : angle 4.42132 ( 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 91 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.425 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: B 37 LEU cc_start: 0.7298 (tp) cc_final: 0.6994 (tt) REVERT: P 301 MET cc_start: 0.8212 (mmm) cc_final: 0.7790 (mmm) REVERT: P 521 HIS cc_start: 0.6375 (t70) cc_final: 0.6166 (t70) REVERT: P 575 GLU cc_start: 0.7483 (mt-10) cc_final: 0.6771 (mt-10) REVERT: P 618 HIS cc_start: 0.6099 (OUTLIER) cc_final: 0.5712 (t-170) outliers start: 13 outliers final: 11 residues processed: 85 average time/residue: 0.2359 time to fit residues: 27.4295 Evaluate side-chains 87 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain P residue 108 ILE Chi-restraints excluded: chain P residue 397 MET Chi-restraints excluded: chain P residue 448 ARG Chi-restraints excluded: chain P residue 484 LEU Chi-restraints excluded: chain P residue 492 LEU Chi-restraints excluded: chain P residue 590 ASP Chi-restraints excluded: chain P residue 618 HIS Chi-restraints excluded: chain P residue 709 ILE 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: 5.9990 chunk 59 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 43 optimal weight: 0.2980 chunk 42 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.118141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.092341 restraints weight = 66147.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.096152 restraints weight = 28617.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.098501 restraints weight = 17789.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.099982 restraints weight = 13518.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.100877 restraints weight = 11441.711| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.6533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9302 Z= 0.127 Angle : 0.563 9.680 12894 Z= 0.309 Chirality : 0.038 0.211 1434 Planarity : 0.004 0.049 1352 Dihedral : 22.952 175.881 2024 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.54 % Favored : 95.35 % Rotamer: Outliers : 1.14 % Allowed : 12.25 % Favored : 86.62 % 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 aren not related in a simple way. whole: 0.64 (0.29), residues: 882 helix: 2.04 (0.25), residues: 409 sheet: -1.18 (0.48), residues: 90 loop : -0.98 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 153 TYR 0.009 0.001 TYR B 46 PHE 0.019 0.001 PHE P 318 TRP 0.014 0.001 TRP P 724 HIS 0.003 0.001 HIS P 241 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9302) covalent geometry : angle 0.56296 (12894) hydrogen bonds : bond 0.03967 ( 436) hydrogen bonds : angle 4.33265 ( 1167) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3046.43 seconds wall clock time: 52 minutes 40.12 seconds (3160.12 seconds total)