Starting phenix.real_space_refine on Fri Jul 3 23:40:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cf1_45526/07_2026/9cf1_45526_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cf1_45526/07_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_45526/07_2026/9cf1_45526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cf1_45526/07_2026/9cf1_45526.map" model { file = "/net/cci-nas-00/data/ceres_data/9cf1_45526/07_2026/9cf1_45526_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cf1_45526/07_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-dev-6108/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: 2.44, per 1000 atoms: 0.14 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: 1.40 Conformation dependent library (CDL) restraints added in 444.9 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: 2.87 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: 4.49 Time building geometry restraints manager: 1.92 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: 27756 2.85 - 5.70: 3137 5.70 - 8.55: 714 8.55 - 11.40: 21 11.40 - 14.25: 14 Bond angle restraints: 31642 Sorted by residual: 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=" N6 A W 41 " pdb=" C6 A W 41 " pdb=" N1 A W 41 " ideal model delta sigma weight residual 118.60 112.53 6.07 6.00e-01 2.78e+00 1.02e+02 angle pdb=" N6 DA N -1 " pdb=" C6 DA N -1 " pdb=" N1 DA N -1 " ideal model delta sigma weight residual 118.60 112.59 6.01 6.00e-01 2.78e+00 1.00e+02 angle pdb=" N6 DA N 0 " pdb=" C6 DA N 0 " pdb=" N1 DA N 0 " ideal model delta sigma weight residual 118.60 112.89 5.71 6.00e-01 2.78e+00 9.06e+01 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 ... (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: 1002 0.094 - 0.188: 355 0.188 - 0.281: 62 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: 1.660 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: 0.090 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 18.840 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.950 ------------------------------------------------------------------------------- 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= 0.957 Angle : 1.846 14.246 12894 Z= 1.560 Chirality : 0.097 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 0.01264 / 0.96 ( 9302) covalent geometry : angle 1.84587 / 1.56 (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 : 0.369 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: 0.2758 time to fit residues: 67.4658 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 : 0.428 ------------------------------------------------------------------------------- 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... P 241 HIS P 595 GLN P 665 GLN P 825 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.119710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.094310 restraints weight = 68747.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.098291 restraints weight = 29341.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.100765 restraints weight = 18144.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.102230 restraints weight = 13758.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.102951 restraints weight = 11721.566| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9302 Z= 0.211 Angle : 0.878 10.029 12894 Z= 0.506 Chirality : 0.055 0.485 1434 Planarity : 0.007 0.092 1352 Dihedral : 24.503 179.888 2031 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.08 % Favored : 95.80 % Rotamer: Outliers : 1.64 % Allowed : 9.09 % Favored : 89.27 % 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: -0.91 (0.26), residues: 882 helix: 0.12 (0.24), residues: 406 sheet: -0.92 (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 490 TYR 0.025 0.002 TYR P 349 PHE 0.023 0.002 PHE P 168 TRP 0.018 0.002 TRP P 724 HIS 0.008 0.002 HIS P 671 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.21 ( 9302) covalent geometry : angle 0.87827 / 0.51 (12894) hydrogen bonds : bond 0.06943 / 4.87 ( 436) hydrogen bonds : angle 5.50570 / 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 126 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.440 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: B 35 ARG cc_start: 0.8075 (ttp80) cc_final: 0.7826 (ttp80) REVERT: P 256 LYS cc_start: 0.8239 (tttt) cc_final: 0.8020 (ttmm) REVERT: P 301 MET cc_start: 0.8001 (mmm) cc_final: 0.7679 (mmm) REVERT: P 397 MET cc_start: 0.7002 (ptt) cc_final: 0.6441 (ttp) REVERT: P 535 ARG cc_start: 0.8150 (ptm160) cc_final: 0.7403 (ptt90) REVERT: P 575 GLU cc_start: 0.7305 (mt-10) cc_final: 0.6633 (mt-10) REVERT: P 685 LEU cc_start: 0.8791 (mt) cc_final: 0.8522 (mp) REVERT: P 772 LYS cc_start: 0.7827 (mmtt) cc_final: 0.7588 (mmtt) outliers start: 13 outliers final: 11 residues processed: 122 average time/residue: 0.2973 time to fit residues: 46.2903 Evaluate side-chains 99 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 91 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 = 0.4112 r_free = 0.4112 target = 0.117896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.092253 restraints weight = 67447.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.096035 restraints weight = 28524.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.098330 restraints weight = 17748.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.099722 restraints weight = 13592.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.100418 restraints weight = 11646.290| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9302 Z= 0.212 Angle : 0.749 8.450 12894 Z= 0.437 Chirality : 0.048 0.263 1434 Planarity : 0.006 0.081 1352 Dihedral : 24.187 171.185 2028 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.67 % Favored : 94.22 % Rotamer: Outliers : 1.39 % Allowed : 10.73 % Favored : 87.88 % 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: -0.82 (0.27), residues: 882 helix: 0.40 (0.25), residues: 406 sheet: -1.10 (0.47), residues: 91 loop : -1.39 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 153 TYR 0.017 0.002 TYR P 205 PHE 0.024 0.002 PHE P 158 TRP 0.012 0.002 TRP P 724 HIS 0.008 0.001 HIS P 671 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.21 ( 9302) covalent geometry : angle 0.74950 / 0.44 (12894) hydrogen bonds : bond 0.05726 / 3.91 ( 436) hydrogen bonds : angle 5.25643 / 3.84 ( 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 106 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 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: P 256 LYS cc_start: 0.8242 (tttt) cc_final: 0.8017 (ttmm) REVERT: P 301 MET cc_start: 0.8066 (mmm) cc_final: 0.7718 (mmm) REVERT: P 494 TYR cc_start: 0.8061 (t80) cc_final: 0.7760 (t80) REVERT: P 513 ASN cc_start: 0.8411 (p0) cc_final: 0.8108 (p0) REVERT: P 523 ARG cc_start: 0.7965 (ttp-170) cc_final: 0.7188 (ttm170) REVERT: P 575 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6805 (mt-10) REVERT: P 597 CYS cc_start: 0.6698 (m) cc_final: 0.6298 (m) outliers start: 11 outliers final: 7 residues processed: 102 average time/residue: 0.2929 time to fit residues: 38.6983 Evaluate side-chains 88 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 7 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 80 optimal weight: 0.0870 chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 55 optimal weight: 0.4980 chunk 4 optimal weight: 8.9990 overall best weight: 1.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 300 ASN P 603 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.119310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.093313 restraints weight = 68686.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.097317 restraints weight = 29478.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.099756 restraints weight = 18384.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.101154 restraints weight = 14009.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.101856 restraints weight = 12044.872| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.4317 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= 0.151 Angle : 0.675 8.934 12894 Z= 0.391 Chirality : 0.045 0.231 1434 Planarity : 0.005 0.063 1352 Dihedral : 24.026 177.500 2024 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.31 % Favored : 95.58 % 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 are not related in a simple way. whole: -0.57 (0.27), residues: 882 helix: 0.72 (0.25), residues: 406 sheet: -1.07 (0.47), residues: 91 loop : -1.37 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 652 TYR 0.014 0.001 TYR P 205 PHE 0.021 0.001 PHE P 158 TRP 0.012 0.001 TRP P 724 HIS 0.003 0.001 HIS P 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 ( 9302) covalent geometry : angle 0.67465 / 0.39 (12894) hydrogen bonds : bond 0.04972 / 3.41 ( 436) hydrogen bonds : angle 5.01263 / 3.59 ( 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 101 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.402 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 256 LYS cc_start: 0.8209 (tttt) cc_final: 0.7985 (ttmm) REVERT: P 301 MET cc_start: 0.8055 (mmm) cc_final: 0.7674 (tpt) REVERT: P 494 TYR cc_start: 0.7681 (t80) cc_final: 0.7477 (t80) REVERT: P 523 ARG cc_start: 0.7958 (ttp-170) cc_final: 0.7150 (mtm-85) REVERT: P 535 ARG cc_start: 0.8182 (ptm160) cc_final: 0.7465 (ptt90) REVERT: P 575 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6636 (mt-10) REVERT: P 597 CYS cc_start: 0.6374 (m) cc_final: 0.6112 (m) REVERT: P 756 GLU cc_start: 0.5809 (OUTLIER) cc_final: 0.5147 (pt0) REVERT: P 769 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7517 (t0) REVERT: P 770 LEU cc_start: 0.8282 (mt) cc_final: 0.7861 (mt) outliers start: 13 outliers final: 7 residues processed: 95 average time/residue: 0.2673 time to fit residues: 33.0820 Evaluate side-chains 85 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 96 LEU 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 675 ILE Chi-restraints excluded: chain P residue 709 ILE Chi-restraints excluded: chain P residue 756 GLU Chi-restraints excluded: chain P residue 769 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 6 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.4126 r_free = 0.4126 target = 0.118895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.093009 restraints weight = 66675.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.096953 restraints weight = 28636.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.099322 restraints weight = 17741.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.100801 restraints weight = 13537.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.101570 restraints weight = 11534.329| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9302 Z= 0.152 Angle : 0.637 8.575 12894 Z= 0.373 Chirality : 0.044 0.241 1434 Planarity : 0.005 0.054 1352 Dihedral : 23.836 174.733 2024 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.54 % Favored : 95.35 % Rotamer: Outliers : 1.39 % Allowed : 11.24 % Favored : 87.37 % 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: -0.40 (0.27), residues: 882 helix: 0.89 (0.25), residues: 412 sheet: -1.19 (0.47), residues: 89 loop : -1.29 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 652 TYR 0.020 0.001 TYR P 386 PHE 0.020 0.001 PHE P 158 TRP 0.012 0.001 TRP P 724 HIS 0.003 0.001 HIS P 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 ( 9302) covalent geometry : angle 0.63749 / 0.37 (12894) hydrogen bonds : bond 0.04767 / 3.23 ( 436) hydrogen bonds : angle 4.88553 / 3.53 ( 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 94 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.473 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 256 LYS cc_start: 0.8190 (tttt) cc_final: 0.7979 (ttmm) REVERT: P 301 MET cc_start: 0.8094 (mmm) cc_final: 0.7699 (mmm) REVERT: P 494 TYR cc_start: 0.7841 (t80) cc_final: 0.7526 (t80) REVERT: P 513 ASN cc_start: 0.8103 (p0) cc_final: 0.7884 (p0) REVERT: P 523 ARG cc_start: 0.7988 (ttp-170) cc_final: 0.7179 (mtm-85) REVERT: P 575 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6604 (mt-10) REVERT: P 756 GLU cc_start: 0.5699 (OUTLIER) cc_final: 0.5120 (pt0) outliers start: 11 outliers final: 8 residues processed: 91 average time/residue: 0.2434 time to fit residues: 29.6500 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 : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 96 LEU 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 709 ILE Chi-restraints excluded: chain P residue 756 GLU 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: 10.0000 chunk 34 optimal weight: 7.9990 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: 5.9990 chunk 35 optimal weight: 0.8980 chunk 66 optimal weight: 0.3980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 52 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.118618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.092655 restraints weight = 67936.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.096641 restraints weight = 29629.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.099055 restraints weight = 18502.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.100462 restraints weight = 14132.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.101315 restraints weight = 12111.078| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9302 Z= 0.160 Angle : 0.631 9.648 12894 Z= 0.365 Chirality : 0.043 0.240 1434 Planarity : 0.004 0.047 1352 Dihedral : 23.689 177.172 2024 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.10 % Favored : 94.78 % Rotamer: Outliers : 1.52 % Allowed : 11.49 % Favored : 86.99 % 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: -0.29 (0.27), residues: 882 helix: 1.08 (0.25), residues: 410 sheet: -1.24 (0.47), residues: 89 loop : -1.34 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 652 TYR 0.012 0.001 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 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 ( 9302) covalent geometry : angle 0.63120 / 0.37 (12894) hydrogen bonds : bond 0.04714 / 3.16 ( 436) hydrogen bonds : angle 4.79472 / 3.46 ( 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 : 0.396 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: B 37 LEU cc_start: 0.7697 (mt) cc_final: 0.7481 (tp) REVERT: P 256 LYS cc_start: 0.8178 (tttt) cc_final: 0.7957 (ttmm) REVERT: P 301 MET cc_start: 0.8142 (mmm) cc_final: 0.7736 (mmm) REVERT: P 494 TYR cc_start: 0.7837 (t80) cc_final: 0.7471 (t80) REVERT: P 513 ASN cc_start: 0.8114 (p0) cc_final: 0.7911 (p0) REVERT: P 523 ARG cc_start: 0.7980 (ttp-170) cc_final: 0.7171 (mtm-85) REVERT: P 575 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6613 (mt-10) REVERT: P 756 GLU cc_start: 0.5765 (OUTLIER) cc_final: 0.5079 (pt0) outliers start: 12 outliers final: 9 residues processed: 90 average time/residue: 0.2519 time to fit residues: 29.7275 Evaluate side-chains 88 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 25 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.118681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.092761 restraints weight = 66642.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.096617 restraints weight = 28540.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.099029 restraints weight = 17778.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.100459 restraints weight = 13532.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.101292 restraints weight = 11552.177| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9302 Z= 0.139 Angle : 0.598 8.280 12894 Z= 0.349 Chirality : 0.042 0.239 1434 Planarity : 0.004 0.048 1352 Dihedral : 23.611 176.671 2024 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.54 % Favored : 95.35 % Rotamer: Outliers : 1.26 % Allowed : 11.49 % Favored : 87.25 % 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: -0.08 (0.28), residues: 882 helix: 1.35 (0.25), residues: 403 sheet: -1.15 (0.47), residues: 90 loop : -1.29 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 652 TYR 0.011 0.001 TYR P 205 PHE 0.018 0.001 PHE P 158 TRP 0.012 0.001 TRP P 724 HIS 0.003 0.001 HIS P 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 ( 9302) covalent geometry : angle 0.59815 / 0.35 (12894) hydrogen bonds : bond 0.04548 / 3.03 ( 436) hydrogen bonds : angle 4.70683 / 3.38 ( 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 93 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.446 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: B 37 LEU cc_start: 0.7784 (mt) cc_final: 0.7554 (tp) REVERT: P 256 LYS cc_start: 0.8189 (tttt) cc_final: 0.7905 (ttmm) REVERT: P 301 MET cc_start: 0.8167 (mmm) cc_final: 0.7750 (mmm) REVERT: P 483 VAL cc_start: 0.8959 (t) cc_final: 0.8637 (p) REVERT: P 494 TYR cc_start: 0.7844 (t80) cc_final: 0.7491 (t80) REVERT: P 523 ARG cc_start: 0.7986 (ttp-170) cc_final: 0.7181 (mtm-85) REVERT: P 575 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6656 (mt-10) REVERT: P 756 GLU cc_start: 0.5650 (OUTLIER) cc_final: 0.4956 (pt0) outliers start: 10 outliers final: 8 residues processed: 90 average time/residue: 0.2617 time to fit residues: 31.4223 Evaluate side-chains 87 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 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 410 LEU 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=2.00 ------------------------------------------------------------------------------- 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: 4.9990 chunk 94 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 = 0.4082 r_free = 0.4082 target = 0.116307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.090180 restraints weight = 67849.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.093916 restraints weight = 29796.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.096227 restraints weight = 18775.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.097562 restraints weight = 14441.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.098405 restraints weight = 12451.445| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9302 Z= 0.248 Angle : 0.667 8.364 12894 Z= 0.386 Chirality : 0.044 0.258 1434 Planarity : 0.005 0.049 1352 Dihedral : 23.588 177.414 2024 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.33 % Favored : 94.44 % Rotamer: Outliers : 1.64 % Allowed : 12.50 % Favored : 85.86 % 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: -0.47 (0.27), residues: 882 helix: 1.05 (0.25), residues: 408 sheet: -1.47 (0.46), residues: 90 loop : -1.54 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 561 TYR 0.015 0.002 TYR P 601 PHE 0.027 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 0.00523 / 0.25 ( 9302) covalent geometry : angle 0.66747 / 0.39 (12894) hydrogen bonds : bond 0.05477 / 3.65 ( 436) hydrogen bonds : angle 4.89563 / 3.55 ( 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 92 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.490 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: P 256 LYS cc_start: 0.8199 (tttt) cc_final: 0.7922 (ttmm) REVERT: P 301 MET cc_start: 0.8159 (mmm) cc_final: 0.7740 (mmm) REVERT: P 494 TYR cc_start: 0.8032 (t80) cc_final: 0.7657 (t80) REVERT: P 523 ARG cc_start: 0.8098 (ttp-170) cc_final: 0.7279 (mtm-85) REVERT: P 575 GLU cc_start: 0.7508 (mt-10) cc_final: 0.6821 (mt-10) REVERT: P 756 GLU cc_start: 0.5771 (OUTLIER) cc_final: 0.5255 (pt0) outliers start: 13 outliers final: 9 residues processed: 87 average time/residue: 0.2544 time to fit residues: 29.5900 Evaluate side-chains 86 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain P residue 108 ILE 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 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: 5.9990 chunk 41 optimal weight: 0.7980 chunk 90 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.116345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.090278 restraints weight = 67734.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.093999 restraints weight = 29757.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.096299 restraints weight = 18720.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.097494 restraints weight = 14395.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.098380 restraints weight = 12535.107| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9302 Z= 0.207 Angle : 0.637 8.274 12894 Z= 0.371 Chirality : 0.043 0.257 1434 Planarity : 0.004 0.049 1352 Dihedral : 23.635 177.788 2024 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.90 % Favored : 93.88 % Rotamer: Outliers : 1.26 % Allowed : 13.01 % Favored : 85.73 % 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: 1.04 (0.25), residues: 407 sheet: -1.50 (0.47), residues: 90 loop : -1.67 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG P 652 TYR 0.029 0.002 TYR B 46 PHE 0.020 0.002 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 0.00428 / 0.21 ( 9302) covalent geometry : angle 0.63720 / 0.37 (12894) hydrogen bonds : bond 0.05171 / 3.42 ( 436) hydrogen bonds : angle 4.84587 / 3.48 ( 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 90 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.385 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: 0.8167 (tttt) cc_final: 0.7890 (ttmm) REVERT: P 301 MET cc_start: 0.8180 (mmm) cc_final: 0.7762 (mmm) REVERT: P 494 TYR cc_start: 0.8038 (t80) cc_final: 0.7605 (t80) REVERT: P 575 GLU cc_start: 0.7497 (mt-10) cc_final: 0.6753 (mt-10) REVERT: P 756 GLU cc_start: 0.5815 (OUTLIER) cc_final: 0.5341 (pt0) outliers start: 10 outliers final: 8 residues processed: 86 average time/residue: 0.2421 time to fit residues: 27.7176 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 : 0.444 ------------------------------------------------------------------------------- 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 467 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 79 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.4096 r_free = 0.4096 target = 0.117162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.090922 restraints weight = 68273.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.094736 restraints weight = 30058.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.097091 restraints weight = 18995.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.098499 restraints weight = 14640.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.099328 restraints weight = 12570.115| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.5447 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= 0.166 Angle : 0.617 8.135 12894 Z= 0.356 Chirality : 0.042 0.247 1434 Planarity : 0.004 0.049 1352 Dihedral : 23.652 178.602 2024 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.33 % Favored : 94.44 % Rotamer: Outliers : 1.26 % Allowed : 13.26 % Favored : 85.48 % 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: 1.19 (0.25), residues: 407 sheet: -1.46 (0.48), residues: 90 loop : -1.63 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 839 TYR 0.016 0.001 TYR B 46 PHE 0.033 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 0.00337 / 0.17 ( 9302) covalent geometry : angle 0.61680 / 0.36 (12894) hydrogen bonds : bond 0.04861 / 3.19 ( 436) hydrogen bonds : angle 4.75078 / 3.45 ( 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 89 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.427 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: 0.8177 (mmm) cc_final: 0.7775 (mmm) REVERT: P 494 TYR cc_start: 0.7949 (t80) cc_final: 0.7511 (t80) REVERT: P 575 GLU cc_start: 0.7466 (mt-10) cc_final: 0.6720 (mt-10) REVERT: P 756 GLU cc_start: 0.5693 (OUTLIER) cc_final: 0.5187 (pt0) outliers start: 10 outliers final: 8 residues processed: 86 average time/residue: 0.2343 time to fit residues: 27.2238 Evaluate side-chains 82 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain P residue 804 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 72 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 0.2980 chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 42 optimal weight: 0.0060 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 = 0.4136 r_free = 0.4136 target = 0.119189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.093677 restraints weight = 66931.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.097502 restraints weight = 28456.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.099890 restraints weight = 17610.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.101311 restraints weight = 13377.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.102048 restraints weight = 11402.363| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.5556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9302 Z= 0.120 Angle : 0.578 7.048 12894 Z= 0.333 Chirality : 0.040 0.238 1434 Planarity : 0.004 0.049 1352 Dihedral : 23.665 179.044 2024 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.31 % Favored : 95.58 % Rotamer: Outliers : 0.76 % Allowed : 13.51 % Favored : 85.73 % 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: -0.06 (0.28), residues: 882 helix: 1.45 (0.25), residues: 406 sheet: -1.27 (0.48), residues: 90 loop : -1.38 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 652 TYR 0.020 0.001 TYR B 46 PHE 0.021 0.001 PHE P 318 TRP 0.013 0.001 TRP P 724 HIS 0.006 0.001 HIS P 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.12 ( 9302) covalent geometry : angle 0.57785 / 0.33 (12894) hydrogen bonds : bond 0.04327 / 2.85 ( 436) hydrogen bonds : angle 4.57102 / 3.30 ( 1167) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3052.72 seconds wall clock time: 52 minutes 51.42 seconds (3171.42 seconds total)