Starting phenix.real_space_refine on Thu Aug 6 20:10:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dpb_47101/08_2026/9dpb_47101.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dpb_47101/08_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_47101/08_2026/9dpb_47101.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dpb_47101/08_2026/9dpb_47101.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dpb_47101/08_2026/9dpb_47101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dpb_47101/08_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-2.2rc3-6140/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, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.34, per 1000 atoms: 0.24 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: 0.58 Conformation dependent library (CDL) restraints added in 178.5 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: 1.08 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: 1.58 Time building geometry restraints manager: 0.76 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: 1240 0.050 - 0.100: 242 0.100 - 0.150: 106 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.170 Find NCS groups from input model: 0.160 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:6.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.830 ------------------------------------------------------------------------------- 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= 0.326 Angle : 0.818 26.351 14160 Z= 0.512 Chirality : 0.049 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 0.00507 / 0.33 (10209) covalent geometry : angle 0.81800 / 0.51 (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 : 0.261 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: 0.5849 time to fit residues: 54.4657 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 : 0.265 ------------------------------------------------------------------------------- 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: 50.0000 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.116358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.071322 restraints weight = 18503.760| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.73 r_work: 0.2928 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.0691 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= 0.129 Angle : 0.532 8.757 14160 Z= 0.273 Chirality : 0.037 0.275 1598 Planarity : 0.005 0.048 1549 Dihedral : 19.465 161.335 2350 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.12 % Allowed : 20.51 % 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 : -0.95 (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 0.027 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 0.00297 / 0.13 (10209) covalent geometry : angle 0.53220 / 0.27 (14160) hydrogen bonds : bond 0.05131 / 3.68 ( 431) hydrogen bonds : angle 5.20601 / 3.57 ( 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 94 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 301 GLU cc_start: 0.8766 (tt0) cc_final: 0.8272 (mm-30) REVERT: A 453 GLU cc_start: 0.7800 (mp0) cc_final: 0.7568 (mp0) REVERT: A 469 MET cc_start: 0.8348 (mpt) cc_final: 0.8066 (mpt) REVERT: A 499 TYR cc_start: 0.8244 (m-80) cc_final: 0.7931 (m-80) REVERT: B 192 LYS cc_start: 0.9115 (ttpp) cc_final: 0.8742 (tmmt) REVERT: B 485 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8276 (ttt180) outliers start: 28 outliers final: 11 residues processed: 86 average time/residue: 0.5934 time to fit residues: 54.8550 Evaluate side-chains 74 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 272 ASN 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: 0.9990 chunk 21 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN B 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.115857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.070861 restraints weight = 18479.720| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.73 r_work: 0.2920 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.0868 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= 0.137 Angle : 0.518 8.298 14160 Z= 0.266 Chirality : 0.037 0.158 1598 Planarity : 0.004 0.049 1549 Dihedral : 19.293 161.309 2338 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.79 % Allowed : 21.29 % 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: 0.05 (0.27), residues: 1007 helix: 1.29 (0.27), residues: 370 sheet: -0.25 (0.36), residues: 215 loop : -0.90 (0.30), residues: 422 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 0.028 0.002 PHE B 340 TRP 0.014 0.002 TRP B 547 HIS 0.002 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (10209) covalent geometry : angle 0.51816 / 0.27 (14160) hydrogen bonds : bond 0.04841 / 3.46 ( 431) hydrogen bonds : angle 4.94157 / 3.41 ( 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 91 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 301 GLU cc_start: 0.8754 (tt0) cc_final: 0.8277 (tp30) REVERT: A 453 GLU cc_start: 0.7934 (mp0) cc_final: 0.7568 (mp0) REVERT: A 469 MET cc_start: 0.7991 (mpt) cc_final: 0.7717 (mpt) REVERT: A 499 TYR cc_start: 0.8233 (m-80) cc_final: 0.7925 (m-80) REVERT: B 161 ARG cc_start: 0.8789 (mtm-85) cc_final: 0.8463 (mtm-85) REVERT: B 406 MET cc_start: 0.7055 (pp-130) cc_final: 0.6361 (pmm) REVERT: B 485 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8237 (ttt180) outliers start: 25 outliers final: 11 residues processed: 84 average time/residue: 0.5963 time to fit residues: 53.7356 Evaluate side-chains 74 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 89 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.117226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.073726 restraints weight = 18634.039| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.59 r_work: 0.3032 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10209 Z= 0.128 Angle : 0.506 9.386 14160 Z= 0.260 Chirality : 0.036 0.142 1598 Planarity : 0.004 0.049 1549 Dihedral : 19.203 161.098 2338 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.34 % Allowed : 20.62 % Favored : 76.03 % 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: 1.36 (0.27), residues: 370 sheet: -0.25 (0.36), residues: 215 loop : -0.88 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 161 TYR 0.013 0.001 TYR A 499 PHE 0.028 0.002 PHE A 340 TRP 0.014 0.002 TRP B 547 HIS 0.002 0.000 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (10209) covalent geometry : angle 0.50566 / 0.26 (14160) hydrogen bonds : bond 0.04639 / 3.33 ( 431) hydrogen bonds : angle 4.75593 / 3.28 ( 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 98 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 68 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8258 (m-30) REVERT: A 301 GLU cc_start: 0.8689 (tt0) cc_final: 0.8257 (tp30) REVERT: A 450 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8314 (mp0) REVERT: A 453 GLU cc_start: 0.8026 (mp0) cc_final: 0.7597 (OUTLIER) REVERT: A 499 TYR cc_start: 0.8176 (m-80) cc_final: 0.7857 (m-80) REVERT: B 162 ASN cc_start: 0.9127 (m110) cc_final: 0.8628 (m110) REVERT: B 406 MET cc_start: 0.7123 (pp-130) cc_final: 0.6799 (pp-130) outliers start: 30 outliers final: 10 residues processed: 90 average time/residue: 0.6121 time to fit residues: 59.1738 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 : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP 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 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 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: 5.9990 chunk 39 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 33 optimal weight: 0.0070 chunk 8 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.7600 ------------------------------------------------------------------------------- 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 = 0.4031 r_free = 0.4031 target = 0.117385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.073905 restraints weight = 18570.385| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.57 r_work: 0.3040 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10209 Z= 0.118 Angle : 0.511 10.743 14160 Z= 0.261 Chirality : 0.036 0.148 1598 Planarity : 0.004 0.049 1549 Dihedral : 19.132 160.934 2336 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.23 % Allowed : 21.40 % Favored : 75.36 % 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: 0.12 (0.27), residues: 1007 helix: 1.37 (0.27), residues: 371 sheet: -0.22 (0.37), residues: 214 loop : -0.88 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 442 TYR 0.014 0.001 TYR A 499 PHE 0.027 0.001 PHE B 340 TRP 0.014 0.002 TRP B 547 HIS 0.003 0.000 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (10209) covalent geometry : angle 0.51146 / 0.26 (14160) hydrogen bonds : bond 0.04532 / 3.26 ( 431) hydrogen bonds : angle 4.65236 / 3.21 ( 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: 29 poor density : 66 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8255 (m-30) REVERT: A 292 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8073 (pmt) REVERT: A 301 GLU cc_start: 0.8702 (tt0) cc_final: 0.8262 (tp30) REVERT: A 451 PHE cc_start: 0.9163 (m-80) cc_final: 0.8412 (m-80) REVERT: A 453 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: A 499 TYR cc_start: 0.8128 (m-80) cc_final: 0.7795 (m-80) REVERT: B 161 ARG cc_start: 0.8604 (mtm-85) cc_final: 0.8296 (mtm-85) REVERT: B 162 ASN cc_start: 0.9084 (m-40) cc_final: 0.8600 (m110) REVERT: B 212 MET cc_start: 0.8866 (ttp) cc_final: 0.8583 (ttm) REVERT: B 406 MET cc_start: 0.7040 (pp-130) cc_final: 0.6658 (pp-130) outliers start: 29 outliers final: 11 residues processed: 88 average time/residue: 0.5683 time to fit residues: 54.0106 Evaluate side-chains 79 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 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 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 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: 0.4980 chunk 49 optimal weight: 2.9990 chunk 104 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 100 optimal weight: 50.0000 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.116958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.073054 restraints weight = 18678.612| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.59 r_work: 0.3001 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10209 Z= 0.196 Angle : 0.554 12.065 14160 Z= 0.281 Chirality : 0.038 0.141 1598 Planarity : 0.005 0.051 1549 Dihedral : 19.112 160.581 2336 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.79 % Allowed : 21.85 % Favored : 75.36 % 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: 1.33 (0.27), residues: 370 sheet: -0.26 (0.37), residues: 215 loop : -0.86 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 442 TYR 0.017 0.001 TYR A 499 PHE 0.032 0.002 PHE A 340 TRP 0.015 0.003 TRP B 547 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 (10209) covalent geometry : angle 0.55411 / 0.28 (14160) hydrogen bonds : bond 0.04744 / 3.38 ( 431) hydrogen bonds : angle 4.70300 / 3.25 ( 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 90 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8239 (m-30) REVERT: A 301 GLU cc_start: 0.8709 (tt0) cc_final: 0.8260 (tp30) REVERT: A 453 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: A 469 MET cc_start: 0.7107 (OUTLIER) cc_final: 0.6838 (mpt) REVERT: A 499 TYR cc_start: 0.8219 (m-80) cc_final: 0.7972 (m-80) REVERT: B 161 ARG cc_start: 0.8580 (mtm-85) cc_final: 0.8062 (mtm-85) REVERT: B 162 ASN cc_start: 0.9211 (m-40) cc_final: 0.8462 (m110) REVERT: B 406 MET cc_start: 0.6914 (pp-130) cc_final: 0.6473 (pp-130) outliers start: 25 outliers final: 11 residues processed: 83 average time/residue: 0.5567 time to fit residues: 49.8456 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 : 0.247 ------------------------------------------------------------------------------- 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 453 GLU Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 87 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 99 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.116143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.072192 restraints weight = 18511.789| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.58 r_work: 0.2992 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10209 Z= 0.148 Angle : 0.532 13.451 14160 Z= 0.269 Chirality : 0.037 0.144 1598 Planarity : 0.004 0.050 1549 Dihedral : 19.072 160.879 2335 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.79 % Allowed : 22.07 % 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: 1.35 (0.27), residues: 370 sheet: -0.35 (0.37), residues: 217 loop : -0.82 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 442 TYR 0.017 0.001 TYR A 499 PHE 0.029 0.002 PHE A 340 TRP 0.015 0.003 TRP B 547 HIS 0.003 0.001 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (10209) covalent geometry : angle 0.53175 / 0.27 (14160) hydrogen bonds : bond 0.04588 / 3.27 ( 431) hydrogen bonds : angle 4.62443 / 3.20 ( 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 89 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 64 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.8234 (m-30) REVERT: A 292 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8072 (pmt) REVERT: A 301 GLU cc_start: 0.8727 (tt0) cc_final: 0.8215 (tp30) REVERT: A 453 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7665 (mp0) REVERT: A 469 MET cc_start: 0.7119 (OUTLIER) cc_final: 0.6851 (mpt) REVERT: A 499 TYR cc_start: 0.8234 (m-80) cc_final: 0.7919 (m-80) REVERT: B 161 ARG cc_start: 0.8661 (mtm-85) cc_final: 0.8087 (mtm-85) REVERT: B 162 ASN cc_start: 0.9227 (m-40) cc_final: 0.8426 (m110) REVERT: B 406 MET cc_start: 0.6928 (pp-130) cc_final: 0.6461 (pp-130) outliers start: 25 outliers final: 10 residues processed: 81 average time/residue: 0.5484 time to fit residues: 47.9424 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 : 0.284 ------------------------------------------------------------------------------- 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 292 MET Chi-restraints excluded: chain A residue 439 THR 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 512 PHE Chi-restraints excluded: chain B residue 87 LEU 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: 0.6980 chunk 105 optimal weight: 50.0000 chunk 68 optimal weight: 0.3980 chunk 6 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 72 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 = 0.3996 r_free = 0.3996 target = 0.116010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.072084 restraints weight = 18443.838| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.58 r_work: 0.2992 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10209 Z= 0.154 Angle : 0.543 13.593 14160 Z= 0.274 Chirality : 0.037 0.142 1598 Planarity : 0.004 0.050 1549 Dihedral : 19.014 160.755 2333 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.79 % Allowed : 22.52 % Favored : 74.69 % 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: 0.12 (0.27), residues: 1007 helix: 1.36 (0.27), residues: 370 sheet: -0.33 (0.37), residues: 216 loop : -0.79 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 442 TYR 0.017 0.001 TYR A 499 PHE 0.030 0.002 PHE A 340 TRP 0.015 0.003 TRP B 547 HIS 0.004 0.001 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 (10209) covalent geometry : angle 0.54326 / 0.27 (14160) hydrogen bonds : bond 0.04588 / 3.27 ( 431) hydrogen bonds : angle 4.63403 / 3.21 ( 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 87 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.8228 (m-30) REVERT: A 292 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8023 (pmt) REVERT: A 301 GLU cc_start: 0.8735 (tt0) cc_final: 0.8223 (tp30) REVERT: A 453 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: A 499 TYR cc_start: 0.8241 (m-80) cc_final: 0.7932 (m-80) REVERT: B 161 ARG cc_start: 0.8675 (mtm-85) cc_final: 0.8467 (mpp80) REVERT: B 162 ASN cc_start: 0.9247 (m-40) cc_final: 0.8923 (m110) REVERT: B 212 MET cc_start: 0.8896 (ttp) cc_final: 0.8572 (ttm) REVERT: B 406 MET cc_start: 0.6971 (pp-130) cc_final: 0.6455 (pp-130) REVERT: B 499 TYR cc_start: 0.8500 (m-10) cc_final: 0.8083 (m-80) outliers start: 25 outliers final: 10 residues processed: 80 average time/residue: 0.5821 time to fit residues: 50.3572 Evaluate side-chains 75 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 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 512 PHE Chi-restraints excluded: chain B residue 87 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 52 optimal weight: 0.1980 chunk 76 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 30 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 = 0.4009 r_free = 0.4009 target = 0.116816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.073180 restraints weight = 18481.079| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.57 r_work: 0.3012 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10209 Z= 0.115 Angle : 0.538 13.775 14160 Z= 0.269 Chirality : 0.036 0.158 1598 Planarity : 0.004 0.049 1549 Dihedral : 18.965 160.835 2333 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.23 % Allowed : 22.63 % 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: 0.18 (0.27), residues: 1007 helix: 1.44 (0.27), residues: 369 sheet: -0.25 (0.37), residues: 214 loop : -0.81 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 442 TYR 0.018 0.001 TYR A 499 PHE 0.027 0.001 PHE B 340 TRP 0.015 0.003 TRP B 547 HIS 0.004 0.000 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (10209) covalent geometry : angle 0.53834 / 0.27 (14160) hydrogen bonds : bond 0.04414 / 3.17 ( 431) hydrogen bonds : angle 4.53265 / 3.14 ( 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 83 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.8227 (m-30) REVERT: A 292 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8078 (pmt) REVERT: A 301 GLU cc_start: 0.8712 (tt0) cc_final: 0.8190 (tp30) REVERT: A 453 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: A 499 TYR cc_start: 0.8213 (m-80) cc_final: 0.7920 (m-80) REVERT: B 161 ARG cc_start: 0.8673 (mtm-85) cc_final: 0.8451 (mpp80) REVERT: B 162 ASN cc_start: 0.9248 (m-40) cc_final: 0.8913 (m110) REVERT: B 406 MET cc_start: 0.6936 (pp-130) cc_final: 0.6382 (pp-130) REVERT: B 499 TYR cc_start: 0.8423 (m-10) cc_final: 0.8072 (m-80) outliers start: 20 outliers final: 9 residues processed: 78 average time/residue: 0.6156 time to fit residues: 51.7552 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 : 0.264 ------------------------------------------------------------------------------- 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 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 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 484 GLU 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: 0.6980 chunk 69 optimal weight: 0.8980 chunk 71 optimal weight: 0.2980 chunk 54 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.116979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.073133 restraints weight = 18334.191| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.57 r_work: 0.3012 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10209 Z= 0.117 Angle : 0.551 13.855 14160 Z= 0.273 Chirality : 0.038 0.376 1598 Planarity : 0.004 0.050 1549 Dihedral : 18.921 160.579 2333 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.90 % Allowed : 23.19 % 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: 0.22 (0.27), residues: 1007 helix: 1.49 (0.27), residues: 369 sheet: -0.17 (0.37), residues: 210 loop : -0.83 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 442 TYR 0.017 0.001 TYR A 499 PHE 0.026 0.001 PHE B 340 TRP 0.015 0.003 TRP B 547 HIS 0.003 0.000 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (10209) covalent geometry : angle 0.55076 / 0.27 (14160) hydrogen bonds : bond 0.04405 / 3.16 ( 431) hydrogen bonds : angle 4.49726 / 3.12 ( 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: 17 poor density : 64 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.8242 (m-30) REVERT: A 292 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8115 (pmt) REVERT: A 301 GLU cc_start: 0.8705 (tt0) cc_final: 0.8203 (tp30) REVERT: A 453 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: A 499 TYR cc_start: 0.8215 (m-80) cc_final: 0.7928 (m-80) REVERT: B 161 ARG cc_start: 0.8708 (mtm-85) cc_final: 0.8460 (mpp80) REVERT: B 162 ASN cc_start: 0.9234 (m110) cc_final: 0.8943 (m110) REVERT: B 406 MET cc_start: 0.7160 (pp-130) cc_final: 0.6566 (pp-130) REVERT: B 499 TYR cc_start: 0.8434 (m-10) cc_final: 0.8090 (m-80) outliers start: 17 outliers final: 11 residues processed: 77 average time/residue: 0.6142 time to fit residues: 50.8945 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 : 0.354 ------------------------------------------------------------------------------- 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 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 484 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 75 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.116657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.072994 restraints weight = 18430.315| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.56 r_work: 0.3008 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1401 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= 0.133 Angle : 0.544 13.634 14160 Z= 0.272 Chirality : 0.037 0.217 1598 Planarity : 0.004 0.048 1549 Dihedral : 18.895 160.358 2333 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.56 % Allowed : 22.74 % Favored : 74.69 % 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: 0.18 (0.27), residues: 1007 helix: 1.45 (0.27), residues: 369 sheet: -0.24 (0.37), residues: 212 loop : -0.82 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 442 TYR 0.017 0.001 TYR A 499 PHE 0.029 0.002 PHE A 340 TRP 0.015 0.003 TRP B 547 HIS 0.004 0.001 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (10209) covalent geometry : angle 0.54432 / 0.27 (14160) hydrogen bonds : bond 0.04428 / 3.17 ( 431) hydrogen bonds : angle 4.50537 / 3.13 ( 1227) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3073.78 seconds wall clock time: 53 minutes 3.86 seconds (3183.86 seconds total)