Starting phenix.real_space_refine on Sat Jul 4 00:20:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dpb_47101/07_2026/9dpb_47101.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dpb_47101/07_2026/9dpb_47101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dpb_47101/07_2026/9dpb_47101.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dpb_47101/07_2026/9dpb_47101.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dpb_47101/07_2026/9dpb_47101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dpb_47101/07_2026/9dpb_47101.map" } resolution = 2.9 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= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9120 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians P 79 5.49 5 Mg 4 5.21 5 S 56 5.16 5 Na 1 4.78 5 C 5970 2.51 5 N 1680 2.21 5 O 2046 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 9836 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 4100 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 29, 'TRANS': 476} Chain: "B" Number of atoms: 4092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 4092 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 29, 'TRANS': 475} Chain: "C" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1557 Classifications: {'RNA': 73} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 4, 'rna3p_pur': 29, 'rna3p_pyr': 32} Link IDs: {'rna2p': 11, 'rna3p': 61} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'APC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'APC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Time building chain proxies: 2.55, per 1000 atoms: 0.26 Number of scatterers: 9836 At special positions: 0 Unit cell: (85.6, 103.79, 141.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 56 16.00 P 79 15.00 Mg 4 11.99 Na 1 11.00 O 2046 8.00 N 1680 7.00 C 5970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 335.5 milliseconds 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1898 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 10 sheets defined 38.7% alpha, 24.1% beta 26 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 75 through 90 Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 238 through 261 removed outlier: 3.782A pdb=" N GLN A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 311 Processing helix chain 'A' and resid 346 through 367 removed outlier: 4.300A pdb=" N GLU A 352 " --> pdb=" O HIS A 348 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE A 353 " --> pdb=" O ASP A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 405 Processing helix chain 'A' and resid 410 through 415 removed outlier: 4.466A pdb=" N GLU A 415 " --> pdb=" O ASN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 430 Processing helix chain 'A' and resid 439 through 452 Processing helix chain 'A' and resid 453 through 456 Processing helix chain 'A' and resid 504 through 521 Processing helix chain 'A' and resid 530 through 538 removed outlier: 3.724A pdb=" N GLU A 538 " --> pdb=" O CYS A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 559 Processing helix chain 'A' and resid 563 through 567 Processing helix chain 'B' and resid 73 through 90 removed outlier: 3.533A pdb=" N ASN B 90 " --> pdb=" O GLN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.669A pdb=" N ASN B 174 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 229 Processing helix chain 'B' and resid 229 through 237 Processing helix chain 'B' and resid 238 through 261 removed outlier: 3.614A pdb=" N GLN B 242 " --> pdb=" O ASP B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 311 Processing helix chain 'B' and resid 348 through 367 removed outlier: 4.435A pdb=" N GLU B 352 " --> pdb=" O HIS B 348 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE B 353 " --> pdb=" O ASP B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 405 Processing helix chain 'B' and resid 416 through 430 removed outlier: 3.538A pdb=" N ARG B 420 " --> pdb=" O THR B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 452 Processing helix chain 'B' and resid 468 through 470 No H-bonds generated for 'chain 'B' and resid 468 through 470' Processing helix chain 'B' and resid 504 through 522 Processing helix chain 'B' and resid 530 through 539 Processing helix chain 'B' and resid 551 through 559 Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 137 removed outlier: 5.862A pdb=" N ILE A 132 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG A 148 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA A 134 " --> pdb=" O ASP A 146 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N LYS A 153 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N ILE A 198 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLN A 155 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N MET A 157 " --> pdb=" O PRO A 200 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N GLU A 202 " --> pdb=" O MET A 157 " (cutoff:3.500A) removed outlier: 10.160A pdb=" N ASN A 159 " --> pdb=" O GLU A 202 " (cutoff:3.500A) removed outlier: 12.610A pdb=" N THR A 204 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE A 198 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY A 189 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASN A 187 " --> pdb=" O PRO A 200 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE A 181 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 264 through 265 removed outlier: 5.932A pdb=" N LEU A 264 " --> pdb=" O TYR A 316 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N ILE A 318 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE A 495 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N GLU A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL A 490 " --> pdb=" O GLU A 494 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS A 496 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ARG A 392 " --> pdb=" O PHE A 461 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 271 through 272 Processing sheet with id=AA4, first strand: chain 'A' and resid 370 through 373 Processing sheet with id=AA5, first strand: chain 'A' and resid 465 through 466 removed outlier: 3.889A pdb=" N HIS A 465 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 159 removed outlier: 3.919A pdb=" N ALA B 134 " --> pdb=" O ASP B 146 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARG B 148 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ILE B 132 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE B 181 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU B 205 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY B 183 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILE B 203 " --> pdb=" O GLY B 183 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLN B 185 " --> pdb=" O TYR B 201 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 264 through 265 removed outlier: 5.854A pdb=" N LEU B 264 " --> pdb=" O TYR B 316 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ILE B 318 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 495 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N GLU B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL B 490 " --> pdb=" O GLU B 494 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N CYS B 496 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLU B 484 " --> pdb=" O THR B 500 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG B 392 " --> pdb=" O PHE B 461 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 264 through 265 removed outlier: 5.854A pdb=" N LEU B 264 " --> pdb=" O TYR B 316 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ILE B 318 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 495 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N GLU B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL B 490 " --> pdb=" O GLU B 494 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N CYS B 496 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLU B 484 " --> pdb=" O THR B 500 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N HIS B 465 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 271 through 272 Processing sheet with id=AB1, first strand: chain 'B' and resid 370 through 373 388 hydrogen bonds defined for protein. 1119 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2116 1.33 - 1.45: 2612 1.45 - 1.58: 5230 1.58 - 1.70: 151 1.70 - 1.82: 100 Bond restraints: 10209 Sorted by residual: bond pdb=" C PRO B 375 " pdb=" N ASP B 376 " ideal model delta sigma weight residual 1.332 1.207 0.125 1.40e-02 5.10e+03 7.99e+01 bond pdb=" C GLY B 405 " pdb=" N MET B 406 " ideal model delta sigma weight residual 1.330 1.407 -0.077 1.53e-02 4.27e+03 2.56e+01 bond pdb=" C THR B 191 " pdb=" N LYS B 192 " ideal model delta sigma weight residual 1.335 1.401 -0.066 1.31e-02 5.83e+03 2.56e+01 bond pdb=" C GLY A 405 " pdb=" N MET A 406 " ideal model delta sigma weight residual 1.329 1.398 -0.068 1.36e-02 5.41e+03 2.51e+01 bond pdb=" C LYS B 135 " pdb=" N ARG B 136 " ideal model delta sigma weight residual 1.330 1.396 -0.065 1.45e-02 4.76e+03 2.03e+01 ... (remaining 10204 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.27: 14139 5.27 - 10.54: 17 10.54 - 15.81: 2 15.81 - 21.08: 0 21.08 - 26.35: 2 Bond angle restraints: 14160 Sorted by residual: angle pdb=" PB APC B 602 " pdb=" O3B APC B 602 " pdb=" PG APC B 602 " ideal model delta sigma weight residual 106.84 133.19 -26.35 3.00e+00 1.11e-01 7.72e+01 angle pdb=" PB APC A 602 " pdb=" O3B APC A 602 " pdb=" PG APC A 602 " ideal model delta sigma weight residual 106.84 131.47 -24.63 3.00e+00 1.11e-01 6.74e+01 angle pdb=" O PRO B 375 " pdb=" C PRO B 375 " pdb=" N ASP B 376 " ideal model delta sigma weight residual 122.38 115.08 7.30 1.39e+00 5.18e-01 2.76e+01 angle pdb=" C5' APC B 602 " pdb=" O5' APC B 602 " pdb=" PA APC B 602 " ideal model delta sigma weight residual 106.85 122.55 -15.70 3.00e+00 1.11e-01 2.74e+01 angle pdb=" C5' APC A 602 " pdb=" O5' APC A 602 " pdb=" PA APC A 602 " ideal model delta sigma weight residual 106.85 122.21 -15.36 3.00e+00 1.11e-01 2.62e+01 ... (remaining 14155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.38: 5881 32.38 - 64.76: 412 64.76 - 97.14: 40 97.14 - 129.52: 2 129.52 - 161.90: 1 Dihedral angle restraints: 6336 sinusoidal: 3385 harmonic: 2951 Sorted by residual: dihedral pdb=" O4' U C 20 " pdb=" C1' U C 20 " pdb=" N1 U C 20 " pdb=" C2 U C 20 " ideal model delta sinusoidal sigma weight residual 200.00 38.10 161.90 1 1.50e+01 4.44e-03 8.32e+01 dihedral pdb=" CA ILE A 462 " pdb=" C ILE A 462 " pdb=" N CYS A 463 " pdb=" CA CYS A 463 " ideal model delta harmonic sigma weight residual 180.00 -156.15 -23.85 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA TYR B 499 " pdb=" C TYR B 499 " pdb=" N THR B 500 " pdb=" CA THR B 500 " ideal model delta harmonic sigma weight residual 180.00 156.70 23.30 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 6333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1316 0.050 - 0.100: 228 0.100 - 0.150: 44 0.150 - 0.200: 8 0.200 - 0.250: 2 Chirality restraints: 1598 Sorted by residual: chirality pdb=" CG LEU B 329 " pdb=" CB LEU B 329 " pdb=" CD1 LEU B 329 " pdb=" CD2 LEU B 329 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CG LEU A 444 " pdb=" CB LEU A 444 " pdb=" CD1 LEU A 444 " pdb=" CD2 LEU A 444 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE B 462 " pdb=" N ILE B 462 " pdb=" C ILE B 462 " pdb=" CB ILE B 462 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.79e-01 ... (remaining 1595 not shown) Planarity restraints: 1549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 376 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.03e+00 pdb=" C ASP B 376 " 0.052 2.00e-02 2.50e+03 pdb=" O ASP B 376 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY B 377 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 388 " -0.032 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO A 389 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 389 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 389 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 468 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.18e+00 pdb=" C ILE B 468 " -0.031 2.00e-02 2.50e+03 pdb=" O ILE B 468 " 0.012 2.00e-02 2.50e+03 pdb=" N MET B 469 " 0.010 2.00e-02 2.50e+03 ... (remaining 1546 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1668 2.76 - 3.30: 9423 3.30 - 3.83: 17982 3.83 - 4.37: 21263 4.37 - 4.90: 34339 Nonbonded interactions: 84675 Sorted by model distance: nonbonded pdb=" N GLU B 195 " pdb=" OE1 GLU B 195 " model vdw 2.231 3.120 nonbonded pdb=" N GLU A 453 " pdb=" OE1 GLU A 453 " model vdw 2.252 3.120 nonbonded pdb=" OD2 ASP B 222 " pdb=" OG1 THR B 225 " model vdw 2.258 3.040 nonbonded pdb=" OE2 GLU A 494 " pdb="MG MG A 603 " model vdw 2.258 2.170 nonbonded pdb=" OH TYR B 286 " pdb=" OD1 ASP B 291 " model vdw 2.279 3.040 ... (remaining 84670 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 72 through 576 or resid 601 through 604)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.110 Find NCS groups from input model: 0.170 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:7.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 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 : 0.005 0.125 10209 Z= 0.323 Angle : 0.770 26.351 14160 Z= 0.467 Chirality : 0.041 0.250 1598 Planarity : 0.005 0.048 1549 Dihedral : 19.843 161.904 4438 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.45 % Allowed : 22.19 % Favored : 76.37 % 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: -0.31 (0.27), residues: 1007 helix: 0.88 (0.27), residues: 366 sheet: -0.28 (0.36), residues: 211 loop : -1.06 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 161 TYR 0.010 0.001 TYR A 316 PHE 0.026 0.001 PHE B 340 TRP 0.015 0.003 TRP B 547 HIS 0.011 0.001 HIS B 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.32 (10209) covalent geometry : angle 0.76955 / 0.47 (14160) hydrogen bonds : bond 0.11241 / 7.71 ( 431) hydrogen bonds : angle 6.44685 / 4.41 ( 1227) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 469 MET cc_start: 0.8014 (mpt) cc_final: 0.7776 (mpt) outliers start: 13 outliers final: 10 residues processed: 87 average time/residue: 0.6637 time to fit residues: 61.7624 Evaluate side-chains 71 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 529 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.0370 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0870 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 50.0000 chunk 106 optimal weight: 40.0000 chunk 38 optimal weight: 0.7980 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 229 GLN A 288 ASN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.116403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.071290 restraints weight = 18491.847| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.73 r_work: 0.2929 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.0692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10209 Z= 0.128 Angle : 0.530 8.841 14160 Z= 0.273 Chirality : 0.037 0.274 1598 Planarity : 0.005 0.048 1549 Dihedral : 19.549 160.904 2350 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.23 % Allowed : 20.40 % Favored : 76.37 % 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: 0.03 (0.27), residues: 1007 helix: 1.27 (0.27), residues: 370 sheet: -0.20 (0.37), residues: 211 loop : -0.94 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 161 TYR 0.011 0.001 TYR A 499 PHE 0.028 0.002 PHE B 340 TRP 0.014 0.002 TRP B 547 HIS 0.004 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (10209) covalent geometry : angle 0.52976 / 0.27 (14160) hydrogen bonds : bond 0.05069 / 3.63 ( 431) hydrogen bonds : angle 5.19482 / 3.56 ( 1227) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 301 GLU cc_start: 0.8761 (tt0) cc_final: 0.8274 (mm-30) REVERT: A 453 GLU cc_start: 0.7813 (mp0) cc_final: 0.7578 (mp0) REVERT: A 469 MET cc_start: 0.8345 (mpt) cc_final: 0.8067 (mpt) REVERT: A 499 TYR cc_start: 0.8239 (m-80) cc_final: 0.7934 (m-80) REVERT: B 192 LYS cc_start: 0.9129 (ttpp) cc_final: 0.8751 (tmmt) REVERT: B 485 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8276 (ttt180) outliers start: 29 outliers final: 10 residues processed: 86 average time/residue: 0.6122 time to fit residues: 56.6666 Evaluate side-chains 73 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 485 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 32 optimal weight: 5.9990 chunk 100 optimal weight: 50.0000 chunk 56 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 26 optimal weight: 0.0370 chunk 70 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.116310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.071346 restraints weight = 18460.578| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.73 r_work: 0.2930 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10209 Z= 0.120 Angle : 0.512 8.255 14160 Z= 0.263 Chirality : 0.037 0.159 1598 Planarity : 0.004 0.049 1549 Dihedral : 19.361 160.863 2338 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.01 % Allowed : 21.07 % Favored : 75.92 % 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: 0.07 (0.27), residues: 1007 helix: 1.32 (0.27), residues: 370 sheet: -0.18 (0.36), residues: 211 loop : -0.94 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 161 TYR 0.012 0.001 TYR A 499 PHE 0.027 0.001 PHE B 340 TRP 0.013 0.002 TRP B 547 HIS 0.003 0.001 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (10209) covalent geometry : angle 0.51185 / 0.26 (14160) hydrogen bonds : bond 0.04694 / 3.35 ( 431) hydrogen bonds : angle 4.90132 / 3.38 ( 1227) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8726 (OUTLIER) cc_final: 0.8188 (m-30) REVERT: A 301 GLU cc_start: 0.8767 (tt0) cc_final: 0.8261 (tp30) REVERT: A 453 GLU cc_start: 0.7896 (mp0) cc_final: 0.7524 (mp0) REVERT: A 469 MET cc_start: 0.7952 (mpt) cc_final: 0.7600 (mpt) REVERT: A 499 TYR cc_start: 0.8226 (m-80) cc_final: 0.7928 (m-80) REVERT: B 406 MET cc_start: 0.7132 (pp-130) cc_final: 0.6446 (pmm) REVERT: B 485 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8196 (ttt180) outliers start: 27 outliers final: 12 residues processed: 86 average time/residue: 0.6420 time to fit residues: 59.2911 Evaluate side-chains 76 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 485 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 77 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.116157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.071737 restraints weight = 18703.261| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.61 r_work: 0.3007 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10209 Z= 0.201 Angle : 0.536 9.111 14160 Z= 0.279 Chirality : 0.038 0.141 1598 Planarity : 0.005 0.051 1549 Dihedral : 19.290 160.357 2338 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.12 % Allowed : 20.74 % Favored : 76.14 % 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 are not related in a simple way. whole: 0.08 (0.27), residues: 1007 helix: 1.29 (0.27), residues: 370 sheet: -0.22 (0.37), residues: 213 loop : -0.86 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 161 TYR 0.013 0.002 TYR A 499 PHE 0.032 0.002 PHE A 340 TRP 0.014 0.003 TRP B 547 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 (10209) covalent geometry : angle 0.53606 / 0.28 (14160) hydrogen bonds : bond 0.04863 / 3.45 ( 431) hydrogen bonds : angle 4.85163 / 3.36 ( 1227) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 68 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 301 GLU cc_start: 0.8704 (tt0) cc_final: 0.8305 (tp30) REVERT: A 450 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8336 (mp0) REVERT: A 453 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7648 (OUTLIER) REVERT: A 499 TYR cc_start: 0.8211 (m-80) cc_final: 0.7912 (m-80) REVERT: B 162 ASN cc_start: 0.9105 (m-40) cc_final: 0.8790 (m110) REVERT: B 212 MET cc_start: 0.8881 (ttp) cc_final: 0.8594 (ttm) REVERT: B 406 MET cc_start: 0.7124 (pp-130) cc_final: 0.6798 (pp-130) outliers start: 28 outliers final: 11 residues processed: 90 average time/residue: 0.6260 time to fit residues: 60.7074 Evaluate side-chains 76 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 95 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.117920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.074032 restraints weight = 18566.405| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.58 r_work: 0.3024 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10209 Z= 0.124 Angle : 0.515 10.552 14160 Z= 0.263 Chirality : 0.037 0.151 1598 Planarity : 0.004 0.049 1549 Dihedral : 19.238 160.688 2336 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.34 % Allowed : 21.63 % Favored : 75.03 % 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 are not related in a simple way. whole: 0.10 (0.27), residues: 1007 helix: 1.35 (0.27), residues: 369 sheet: -0.26 (0.37), residues: 214 loop : -0.86 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 442 TYR 0.015 0.001 TYR A 499 PHE 0.028 0.001 PHE B 340 TRP 0.014 0.002 TRP B 547 HIS 0.003 0.001 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (10209) covalent geometry : angle 0.51486 / 0.26 (14160) hydrogen bonds : bond 0.04561 / 3.26 ( 431) hydrogen bonds : angle 4.69686 / 3.24 ( 1227) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8253 (m-30) REVERT: A 301 GLU cc_start: 0.8684 (tt0) cc_final: 0.8260 (tp30) REVERT: A 451 PHE cc_start: 0.9169 (m-80) cc_final: 0.8420 (m-80) REVERT: A 453 GLU cc_start: 0.8020 (mp0) cc_final: 0.7576 (mp0) REVERT: A 499 TYR cc_start: 0.8207 (m-80) cc_final: 0.7898 (m-80) REVERT: B 161 ARG cc_start: 0.8687 (mtm-85) cc_final: 0.8445 (mtm-85) REVERT: B 162 ASN cc_start: 0.9267 (m-40) cc_final: 0.8676 (m110) REVERT: B 212 MET cc_start: 0.8879 (ttp) cc_final: 0.8563 (ttm) REVERT: B 406 MET cc_start: 0.7061 (pp-130) cc_final: 0.6741 (pp-130) outliers start: 30 outliers final: 11 residues processed: 89 average time/residue: 0.6003 time to fit residues: 57.7536 Evaluate side-chains 75 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 490 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 95 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 104 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 60 optimal weight: 0.0980 chunk 93 optimal weight: 0.0770 chunk 100 optimal weight: 40.0000 chunk 38 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.117395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.074313 restraints weight = 18643.777| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.56 r_work: 0.3024 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10209 Z= 0.136 Angle : 0.530 12.295 14160 Z= 0.269 Chirality : 0.037 0.141 1598 Planarity : 0.004 0.050 1549 Dihedral : 19.182 160.440 2335 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.68 % Allowed : 22.19 % Favored : 75.14 % 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 are not related in a simple way. whole: 0.09 (0.27), residues: 1007 helix: 1.34 (0.27), residues: 370 sheet: -0.29 (0.37), residues: 214 loop : -0.86 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 442 TYR 0.015 0.001 TYR A 499 PHE 0.028 0.001 PHE A 340 TRP 0.015 0.002 TRP B 547 HIS 0.003 0.001 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (10209) covalent geometry : angle 0.53011 / 0.27 (14160) hydrogen bonds : bond 0.04524 / 3.23 ( 431) hydrogen bonds : angle 4.64141 / 3.21 ( 1227) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8253 (m-30) REVERT: A 292 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8128 (pmt) REVERT: A 301 GLU cc_start: 0.8707 (tt0) cc_final: 0.8292 (tp30) REVERT: A 453 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: A 469 MET cc_start: 0.7132 (OUTLIER) cc_final: 0.6864 (mpt) REVERT: A 499 TYR cc_start: 0.8207 (m-80) cc_final: 0.7921 (m-80) REVERT: B 161 ARG cc_start: 0.8687 (mtm-85) cc_final: 0.8421 (mtm-85) REVERT: B 162 ASN cc_start: 0.9292 (m-40) cc_final: 0.8827 (m110) REVERT: B 406 MET cc_start: 0.6913 (pp-130) cc_final: 0.6479 (pp-130) REVERT: B 485 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8530 (ttt180) outliers start: 24 outliers final: 13 residues processed: 82 average time/residue: 0.6631 time to fit residues: 58.4059 Evaluate side-chains 81 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 485 ARG Chi-restraints excluded: chain B residue 490 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 99 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.117769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.073841 restraints weight = 18559.971| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.61 r_work: 0.3005 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10209 Z= 0.119 Angle : 0.522 13.544 14160 Z= 0.264 Chirality : 0.037 0.144 1598 Planarity : 0.004 0.049 1549 Dihedral : 19.112 160.282 2335 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.23 % Allowed : 21.63 % Favored : 75.14 % 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 are not related in a simple way. whole: 0.13 (0.27), residues: 1007 helix: 1.40 (0.27), residues: 370 sheet: -0.28 (0.37), residues: 215 loop : -0.84 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 442 TYR 0.020 0.001 TYR A 499 PHE 0.027 0.001 PHE B 340 TRP 0.015 0.002 TRP B 547 HIS 0.003 0.000 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (10209) covalent geometry : angle 0.52185 / 0.26 (14160) hydrogen bonds : bond 0.04408 / 3.16 ( 431) hydrogen bonds : angle 4.54191 / 3.13 ( 1227) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 64 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8246 (m-30) REVERT: A 292 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8026 (pmt) REVERT: A 301 GLU cc_start: 0.8758 (tt0) cc_final: 0.8239 (tp30) REVERT: A 453 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: A 499 TYR cc_start: 0.8196 (m-80) cc_final: 0.7909 (m-80) REVERT: B 161 ARG cc_start: 0.8752 (mtm-85) cc_final: 0.8362 (mtm-85) REVERT: B 162 ASN cc_start: 0.9298 (m-40) cc_final: 0.8499 (m110) REVERT: B 406 MET cc_start: 0.6909 (pp-130) cc_final: 0.6419 (pp-130) outliers start: 29 outliers final: 11 residues processed: 84 average time/residue: 0.6370 time to fit residues: 57.6655 Evaluate side-chains 76 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 490 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 105 optimal weight: 50.0000 chunk 68 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.115114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.071639 restraints weight = 18674.607| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.54 r_work: 0.2972 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 10209 Z= 0.298 Angle : 0.616 13.217 14160 Z= 0.317 Chirality : 0.041 0.141 1598 Planarity : 0.005 0.053 1549 Dihedral : 19.143 159.743 2333 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.90 % Allowed : 22.19 % Favored : 74.92 % 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: -0.09 (0.27), residues: 1007 helix: 1.18 (0.27), residues: 370 sheet: -0.49 (0.36), residues: 221 loop : -0.87 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 442 TYR 0.016 0.002 TYR A 499 PHE 0.037 0.003 PHE A 340 TRP 0.016 0.003 TRP B 547 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00713 / 0.30 (10209) covalent geometry : angle 0.61632 / 0.32 (14160) hydrogen bonds : bond 0.05152 / 3.60 ( 431) hydrogen bonds : angle 4.85313 / 3.37 ( 1227) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 301 GLU cc_start: 0.8688 (tt0) cc_final: 0.8307 (tt0) REVERT: A 453 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7778 (mp0) REVERT: A 469 MET cc_start: 0.7388 (mpp) cc_final: 0.7065 (mpt) REVERT: B 161 ARG cc_start: 0.8701 (mtm-85) cc_final: 0.8295 (mtm-85) REVERT: B 162 ASN cc_start: 0.9284 (m-40) cc_final: 0.8471 (m110) REVERT: B 406 MET cc_start: 0.6957 (pp-130) cc_final: 0.6463 (pp-130) REVERT: B 450 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7542 (mp0) outliers start: 26 outliers final: 12 residues processed: 81 average time/residue: 0.6247 time to fit residues: 54.6189 Evaluate side-chains 77 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 490 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.117044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.073206 restraints weight = 18548.039| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.58 r_work: 0.2992 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10209 Z= 0.123 Angle : 0.543 13.734 14160 Z= 0.275 Chirality : 0.037 0.146 1598 Planarity : 0.004 0.049 1549 Dihedral : 19.096 160.806 2333 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.01 % Allowed : 22.97 % Favored : 75.03 % 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 are not related in a simple way. whole: 0.06 (0.27), residues: 1007 helix: 1.32 (0.27), residues: 370 sheet: -0.44 (0.36), residues: 216 loop : -0.79 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 442 TYR 0.012 0.001 TYR A 316 PHE 0.029 0.002 PHE B 340 TRP 0.015 0.003 TRP B 547 HIS 0.007 0.001 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (10209) covalent geometry : angle 0.54258 / 0.27 (14160) hydrogen bonds : bond 0.04493 / 3.20 ( 431) hydrogen bonds : angle 4.62564 / 3.20 ( 1227) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.8380 (ptt) cc_final: 0.8103 (pmt) REVERT: A 301 GLU cc_start: 0.8708 (tt0) cc_final: 0.8364 (tp30) REVERT: A 453 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: A 469 MET cc_start: 0.7267 (mpp) cc_final: 0.6968 (mpt) REVERT: B 161 ARG cc_start: 0.8758 (mtm-85) cc_final: 0.8463 (mpp80) REVERT: B 162 ASN cc_start: 0.9304 (m-40) cc_final: 0.8813 (m110) REVERT: B 406 MET cc_start: 0.6986 (pp-130) cc_final: 0.6404 (pp-130) outliers start: 18 outliers final: 9 residues processed: 77 average time/residue: 0.6799 time to fit residues: 56.1800 Evaluate side-chains 72 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.115968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.072017 restraints weight = 18370.740| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.57 r_work: 0.2993 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10209 Z= 0.142 Angle : 0.559 13.736 14160 Z= 0.280 Chirality : 0.038 0.362 1598 Planarity : 0.005 0.050 1549 Dihedral : 19.048 160.406 2333 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.12 % Allowed : 22.85 % Favored : 75.03 % 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 are not related in a simple way. whole: 0.10 (0.27), residues: 1007 helix: 1.40 (0.27), residues: 370 sheet: -0.33 (0.36), residues: 210 loop : -0.85 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 442 TYR 0.022 0.001 TYR B 499 PHE 0.028 0.001 PHE B 340 TRP 0.015 0.003 TRP B 547 HIS 0.010 0.001 HIS B 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (10209) covalent geometry : angle 0.55869 / 0.28 (14160) hydrogen bonds : bond 0.04483 / 3.18 ( 431) hydrogen bonds : angle 4.59105 / 3.18 ( 1227) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 MET cc_start: 0.8387 (ptt) cc_final: 0.8073 (pmt) REVERT: A 301 GLU cc_start: 0.8780 (tt0) cc_final: 0.8351 (tp30) REVERT: A 453 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7738 (mp0) REVERT: A 469 MET cc_start: 0.7238 (mpp) cc_final: 0.6937 (mpt) REVERT: B 161 ARG cc_start: 0.8753 (mtm-85) cc_final: 0.8469 (mpp80) REVERT: B 162 ASN cc_start: 0.9306 (m-40) cc_final: 0.8893 (m110) REVERT: B 406 MET cc_start: 0.6973 (pp-130) cc_final: 0.6390 (pp-130) outliers start: 19 outliers final: 12 residues processed: 76 average time/residue: 0.6244 time to fit residues: 51.2728 Evaluate side-chains 74 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain A residue 601 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 75 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.0020 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 19 optimal weight: 0.0770 chunk 6 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.4946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.116996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.073389 restraints weight = 18435.115| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.57 r_work: 0.3018 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10209 Z= 0.106 Angle : 0.542 13.687 14160 Z= 0.272 Chirality : 0.037 0.150 1598 Planarity : 0.004 0.049 1549 Dihedral : 18.986 160.328 2333 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.56 % Allowed : 23.30 % Favored : 75.14 % 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 are not related in a simple way. whole: 0.14 (0.27), residues: 1007 helix: 1.44 (0.27), residues: 369 sheet: -0.30 (0.36), residues: 211 loop : -0.86 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 442 TYR 0.015 0.001 TYR A 499 PHE 0.026 0.001 PHE B 340 TRP 0.016 0.003 TRP B 547 HIS 0.008 0.001 HIS B 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (10209) covalent geometry : angle 0.54222 / 0.27 (14160) hydrogen bonds : bond 0.04321 / 3.09 ( 431) hydrogen bonds : angle 4.50308 / 3.12 ( 1227) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3348.08 seconds wall clock time: 58 minutes 6.27 seconds (3486.27 seconds total)