Starting phenix.real_space_refine on Thu Jul 2 17:15:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7bcw_12145/07_2026/7bcw_12145.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bcw_12145/07_2026/7bcw_12145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bcw_12145/07_2026/7bcw_12145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bcw_12145/07_2026/7bcw_12145.map" model { file = "/net/cci-nas-00/data/ceres_data/7bcw_12145/07_2026/7bcw_12145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bcw_12145/07_2026/7bcw_12145.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7bcw_12145/07_2026/7bcw_12145.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7bcw_12145/07_2026/7bcw_12145.cif" } resolution = 3.5 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= 0.003 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians V 2 8.30 5 P 6 5.49 5 Mg 2 5.21 5 S 54 5.16 5 C 5696 2.51 5 N 1560 2.21 5 O 1705 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 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: 9025 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4452 Classifications: {'peptide': 574} Link IDs: {'PTRANS': 13, 'TRANS': 560} Chain: "B" Number of atoms: 4452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4452 Classifications: {'peptide': 574} Link IDs: {'PTRANS': 13, 'TRANS': 560} Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 65 Unusual residues: {' MG': 1, 'ADP': 1, 'POV': 1, 'VO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {' MG': 1, 'ADP': 1, 'POV': 1, 'VO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'POV:plan-3': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 1.68, per 1000 atoms: 0.19 Number of scatterers: 9025 At special positions: 0 Unit cell: (77.738, 79.392, 141.417, 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) V 2 22.97 S 54 16.00 P 6 15.00 Mg 2 11.99 O 1705 8.00 N 1560 7.00 C 5696 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: 0.81 Conformation dependent library (CDL) restraints added in 231.1 milliseconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 5 sheets defined 67.3% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 Proline residue: A 18 - end of helix Processing helix chain 'A' and resid 24 through 46 removed outlier: 4.212A pdb=" N VAL A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 54 Processing helix chain 'A' and resid 66 through 109 removed outlier: 3.869A pdb=" N VAL A 70 " --> pdb=" O TRP A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 120 through 130 removed outlier: 3.845A pdb=" N LEU A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 141 Processing helix chain 'A' and resid 141 through 164 removed outlier: 3.741A pdb=" N THR A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 213 removed outlier: 3.787A pdb=" N VAL A 173 " --> pdb=" O ILE A 169 " (cutoff:3.500A) Proline residue: A 176 - end of helix removed outlier: 3.759A pdb=" N ARG A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 220 Processing helix chain 'A' and resid 222 through 271 removed outlier: 3.604A pdb=" N GLU A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Proline residue: A 253 - end of helix removed outlier: 3.557A pdb=" N LEU A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ALA A 262 " --> pdb=" O ILE A 258 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 removed outlier: 3.696A pdb=" N ASP A 277 " --> pdb=" O PRO A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 323 removed outlier: 3.796A pdb=" N MET A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ARG A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) Proline residue: A 297 - end of helix removed outlier: 4.552A pdb=" N ALA A 306 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLN A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 389 removed outlier: 3.729A pdb=" N ALA A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 417 Processing helix chain 'A' and resid 432 through 438 Processing helix chain 'A' and resid 446 through 457 Processing helix chain 'A' and resid 459 through 464 removed outlier: 3.541A pdb=" N ASN A 464 " --> pdb=" O MET A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 472 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 488 through 497 removed outlier: 3.531A pdb=" N ALA A 492 " --> pdb=" O ARG A 488 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG A 497 " --> pdb=" O ARG A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 527 Processing helix chain 'A' and resid 561 through 567 Processing helix chain 'A' and resid 570 through 577 Processing helix chain 'B' and resid 8 through 21 Proline residue: B 18 - end of helix Processing helix chain 'B' and resid 24 through 47 removed outlier: 3.659A pdb=" N LEU B 45 " --> pdb=" O ASP B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 54 Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 66 through 109 removed outlier: 4.070A pdb=" N VAL B 92 " --> pdb=" O CYS B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 Processing helix chain 'B' and resid 120 through 141 removed outlier: 3.825A pdb=" N LEU B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER B 132 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 164 removed outlier: 3.732A pdb=" N THR B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 212 removed outlier: 3.661A pdb=" N VAL B 173 " --> pdb=" O ILE B 169 " (cutoff:3.500A) Proline residue: B 176 - end of helix removed outlier: 4.223A pdb=" N ARG B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN B 198 " --> pdb=" O LYS B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 221 removed outlier: 3.599A pdb=" N PHE B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 271 Proline residue: B 253 - end of helix removed outlier: 4.138A pdb=" N ALA B 262 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 323 Proline residue: B 297 - end of helix removed outlier: 4.692A pdb=" N ALA B 306 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N GLN B 307 " --> pdb=" O ASN B 303 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP B 323 " --> pdb=" O PHE B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 391 Processing helix chain 'B' and resid 415 through 417 No H-bonds generated for 'chain 'B' and resid 415 through 417' Processing helix chain 'B' and resid 432 through 438 Processing helix chain 'B' and resid 446 through 457 Processing helix chain 'B' and resid 459 through 464 Processing helix chain 'B' and resid 468 through 472 removed outlier: 3.624A pdb=" N THR B 472 " --> pdb=" O GLY B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 497 removed outlier: 4.052A pdb=" N ARG B 497 " --> pdb=" O ARG B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 524 Processing helix chain 'B' and resid 525 through 529 removed outlier: 3.751A pdb=" N LYS B 528 " --> pdb=" O GLU B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 569 Processing helix chain 'B' and resid 570 through 578 removed outlier: 3.512A pdb=" N GLN B 574 " --> pdb=" O GLY B 570 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 365 through 366 removed outlier: 4.483A pdb=" N VAL A 347 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLU A 397 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 419 through 422 removed outlier: 6.362A pdb=" N ALA A 420 " --> pdb=" O ILE A 503 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ASP A 505 " --> pdb=" O ALA A 420 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL A 422 " --> pdb=" O ASP A 505 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU A 502 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE A 535 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU A 504 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N THR A 371 " --> pdb=" O GLU A 547 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL A 549 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ALA A 373 " --> pdb=" O VAL A 549 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL A 551 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL A 375 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 558 " --> pdb=" O VAL A 550 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLU A 552 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE A 556 " --> pdb=" O GLU A 552 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 359 through 362 removed outlier: 5.990A pdb=" N VAL B 347 " --> pdb=" O ASN B 361 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 359 through 362 removed outlier: 5.990A pdb=" N VAL B 347 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL B 347 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLU B 397 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 419 through 422 removed outlier: 6.598A pdb=" N ALA B 420 " --> pdb=" O ILE B 503 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ASP B 505 " --> pdb=" O ALA B 420 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL B 422 " --> pdb=" O ASP B 505 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU B 502 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ILE B 535 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU B 504 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR B 371 " --> pdb=" O GLU B 547 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL B 549 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ALA B 373 " --> pdb=" O VAL B 549 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 551 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL B 375 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU B 558 " --> pdb=" O VAL B 550 " (cutoff:3.500A) 555 hydrogen bonds defined for protein. 1626 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.22 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 1877 1.33 - 1.47: 3147 1.47 - 1.62: 4013 1.62 - 1.76: 5 1.76 - 1.91: 111 Bond restraints: 9153 Sorted by residual: bond pdb=" C21 POV A 604 " pdb=" O21 POV A 604 " ideal model delta sigma weight residual 1.330 1.404 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C21 POV B 604 " pdb=" O21 POV B 604 " ideal model delta sigma weight residual 1.330 1.404 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C31 POV A 604 " pdb=" O31 POV A 604 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" CB MET A 242 " pdb=" CG MET A 242 " ideal model delta sigma weight residual 1.520 1.469 0.051 3.00e-02 1.11e+03 2.89e+00 bond pdb=" C28 POV B 604 " pdb=" C29 POV B 604 " ideal model delta sigma weight residual 1.497 1.528 -0.031 2.00e-02 2.50e+03 2.35e+00 ... (remaining 9148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 12182 2.50 - 5.01: 152 5.01 - 7.51: 31 7.51 - 10.02: 5 10.02 - 12.52: 4 Bond angle restraints: 12374 Sorted by residual: angle pdb=" O13 POV A 604 " pdb=" P POV A 604 " pdb=" O14 POV A 604 " ideal model delta sigma weight residual 121.11 108.59 12.52 3.00e+00 1.11e-01 1.74e+01 angle pdb=" O11 POV A 604 " pdb=" P POV A 604 " pdb=" O12 POV A 604 " ideal model delta sigma weight residual 97.67 109.98 -12.31 3.00e+00 1.11e-01 1.68e+01 angle pdb=" O13 POV B 604 " pdb=" P POV B 604 " pdb=" O14 POV B 604 " ideal model delta sigma weight residual 121.11 109.01 12.10 3.00e+00 1.11e-01 1.63e+01 angle pdb=" O11 POV B 604 " pdb=" P POV B 604 " pdb=" O12 POV B 604 " ideal model delta sigma weight residual 97.67 109.66 -11.99 3.00e+00 1.11e-01 1.60e+01 angle pdb=" CB MET B 276 " pdb=" CG MET B 276 " pdb=" SD MET B 276 " ideal model delta sigma weight residual 112.70 122.24 -9.54 3.00e+00 1.11e-01 1.01e+01 ... (remaining 12369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.75: 5369 30.75 - 61.50: 164 61.50 - 92.25: 18 92.25 - 123.00: 0 123.00 - 153.75: 5 Dihedral angle restraints: 5556 sinusoidal: 2236 harmonic: 3320 Sorted by residual: dihedral pdb=" O2A ADP B 602 " pdb=" O3A ADP B 602 " pdb=" PA ADP B 602 " pdb=" PB ADP B 602 " ideal model delta sinusoidal sigma weight residual -60.00 73.70 -133.70 1 2.00e+01 2.50e-03 4.06e+01 dihedral pdb=" O1B ADP B 602 " pdb=" O3A ADP B 602 " pdb=" PB ADP B 602 " pdb=" PA ADP B 602 " ideal model delta sinusoidal sigma weight residual -60.00 73.08 -133.08 1 2.00e+01 2.50e-03 4.04e+01 dihedral pdb=" O1B ADP A 602 " pdb=" O3A ADP A 602 " pdb=" PB ADP A 602 " pdb=" PA ADP A 602 " ideal model delta sinusoidal sigma weight residual 300.00 172.88 127.11 1 2.00e+01 2.50e-03 3.85e+01 ... (remaining 5553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 756 0.029 - 0.058: 460 0.058 - 0.087: 167 0.087 - 0.116: 67 0.116 - 0.144: 16 Chirality restraints: 1466 Sorted by residual: chirality pdb=" CA ILE B 400 " pdb=" N ILE B 400 " pdb=" C ILE B 400 " pdb=" CB ILE B 400 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA VAL A 342 " pdb=" N VAL A 342 " pdb=" C VAL A 342 " pdb=" CB VAL A 342 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA ILE B 535 " pdb=" N ILE B 535 " pdb=" C ILE B 535 " pdb=" CB ILE B 535 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 1463 not shown) Planarity restraints: 1552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 67 " -0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO A 68 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 68 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 68 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 542 " -0.008 2.00e-02 2.50e+03 1.47e-02 2.15e+00 pdb=" C ILE A 542 " 0.025 2.00e-02 2.50e+03 pdb=" O ILE A 542 " -0.009 2.00e-02 2.50e+03 pdb=" N GLU A 543 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 175 " 0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO B 176 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 176 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 176 " 0.018 5.00e-02 4.00e+02 ... (remaining 1549 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 43 2.47 - 3.08: 6634 3.08 - 3.69: 13610 3.69 - 4.29: 19418 4.29 - 4.90: 32740 Nonbonded interactions: 72445 Sorted by model distance: nonbonded pdb=" O2 VO4 B 601 " pdb="MG MG B 603 " model vdw 1.868 2.170 nonbonded pdb=" OG SER B 383 " pdb="MG MG B 603 " model vdw 1.889 2.170 nonbonded pdb=" OE1 GLN B 424 " pdb="MG MG B 603 " model vdw 1.942 2.170 nonbonded pdb=" O1B ADP B 602 " pdb="MG MG B 603 " model vdw 1.969 2.170 nonbonded pdb=" OE1 GLN A 424 " pdb="MG MG A 603 " model vdw 2.018 2.170 ... (remaining 72440 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 6 through 603 or (resid 604 and (name C1 or name C2 or nam \ e C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or \ name C28 or name C29 or name C3 or name O11 or name O12 or name O13 or name O14 \ or name O21 or name O22 or name O31)))) selection = (chain 'B' and (resid 6 through 603 or (resid 604 and (name C1 or name C2 or nam \ e C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or \ name C28 or name C29 or name C3 or name O11 or name O12 or name O13 or name O14 \ or name O21 or name O22 or name O31)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.390 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 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 0.074 9153 Z= 0.234 Angle : 0.760 12.522 12374 Z= 0.373 Chirality : 0.043 0.144 1466 Planarity : 0.003 0.047 1552 Dihedral : 15.721 153.755 3408 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.25), residues: 1144 helix: 1.18 (0.20), residues: 714 sheet: -0.10 (0.60), residues: 68 loop : -1.14 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 377 TYR 0.007 0.001 TYR A 83 PHE 0.014 0.001 PHE A 56 TRP 0.010 0.002 TRP B 91 HIS 0.011 0.001 HIS B 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.23 ( 9153) covalent geometry : angle 0.75976 / 0.37 (12374) hydrogen bonds : bond 0.15808 / 11.13 ( 552) hydrogen bonds : angle 5.86845 / 4.31 ( 1626) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.328 Fit side-chains REVERT: A 158 ILE cc_start: 0.8858 (pt) cc_final: 0.8652 (mt) REVERT: B 403 ASP cc_start: 0.7550 (t0) cc_final: 0.7211 (t0) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.0723 time to fit residues: 11.9217 Evaluate side-chains 93 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.0470 chunk 49 optimal weight: 0.3980 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 435 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.119384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.106534 restraints weight = 15265.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.109639 restraints weight = 6699.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.111594 restraints weight = 3715.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.112800 restraints weight = 2435.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.113494 restraints weight = 1819.783| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9153 Z= 0.122 Angle : 0.581 8.101 12374 Z= 0.287 Chirality : 0.040 0.147 1466 Planarity : 0.003 0.034 1552 Dihedral : 9.786 156.297 1302 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.92 % Allowed : 7.16 % Favored : 91.92 % 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: 1.02 (0.25), residues: 1144 helix: 1.60 (0.20), residues: 728 sheet: -0.05 (0.62), residues: 70 loop : -1.16 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 391 TYR 0.011 0.001 TYR A 572 PHE 0.023 0.001 PHE A 43 TRP 0.010 0.001 TRP B 165 HIS 0.008 0.001 HIS B 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 9153) covalent geometry : angle 0.58062 / 0.29 (12374) hydrogen bonds : bond 0.04656 / 3.11 ( 552) hydrogen bonds : angle 4.19174 / 3.09 ( 1626) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.364 Fit side-chains REVERT: A 208 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8234 (tm-30) REVERT: A 210 MET cc_start: 0.8722 (tmm) cc_final: 0.8484 (tmm) REVERT: A 212 LYS cc_start: 0.7839 (tttm) cc_final: 0.7426 (ttpt) REVERT: B 242 MET cc_start: 0.8381 (mmm) cc_final: 0.8161 (mmm) REVERT: B 403 ASP cc_start: 0.7687 (t0) cc_final: 0.7257 (t0) outliers start: 9 outliers final: 3 residues processed: 123 average time/residue: 0.0868 time to fit residues: 15.3675 Evaluate side-chains 104 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 101 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 245 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 39 optimal weight: 0.9980 chunk 10 optimal weight: 0.0270 chunk 14 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.117823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.105276 restraints weight = 15157.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.108343 restraints weight = 6557.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.110236 restraints weight = 3598.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.111248 restraints weight = 2358.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.112112 restraints weight = 1814.175| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9153 Z= 0.114 Angle : 0.561 10.543 12374 Z= 0.271 Chirality : 0.040 0.147 1466 Planarity : 0.003 0.030 1552 Dihedral : 9.440 149.615 1302 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.53 % Allowed : 10.94 % Favored : 87.53 % 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: 1.34 (0.25), residues: 1144 helix: 1.85 (0.20), residues: 728 sheet: 0.01 (0.61), residues: 70 loop : -1.00 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 377 TYR 0.008 0.001 TYR A 572 PHE 0.014 0.001 PHE A 319 TRP 0.007 0.001 TRP B 165 HIS 0.009 0.001 HIS B 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 9153) covalent geometry : angle 0.56118 / 0.27 (12374) hydrogen bonds : bond 0.04207 / 2.80 ( 552) hydrogen bonds : angle 3.88521 / 2.86 ( 1626) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.312 Fit side-chains REVERT: A 208 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8027 (tm-30) REVERT: A 212 LYS cc_start: 0.7826 (tttm) cc_final: 0.6956 (mtpt) REVERT: B 210 MET cc_start: 0.9211 (tmm) cc_final: 0.8917 (tmm) REVERT: B 403 ASP cc_start: 0.7703 (t0) cc_final: 0.7334 (t0) REVERT: B 427 HIS cc_start: 0.6973 (t-90) cc_final: 0.6759 (t70) outliers start: 15 outliers final: 8 residues processed: 118 average time/residue: 0.0878 time to fit residues: 14.9980 Evaluate side-chains 110 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 396 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 72 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 305 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.119264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.106182 restraints weight = 15522.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.109293 restraints weight = 6793.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.111268 restraints weight = 3780.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.112351 restraints weight = 2488.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.113185 restraints weight = 1914.390| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9153 Z= 0.117 Angle : 0.551 9.610 12374 Z= 0.266 Chirality : 0.040 0.134 1466 Planarity : 0.003 0.030 1552 Dihedral : 9.209 140.438 1302 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.25 % Allowed : 11.86 % Favored : 85.89 % 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: 1.51 (0.26), residues: 1144 helix: 2.00 (0.20), residues: 728 sheet: 0.04 (0.61), residues: 70 loop : -0.99 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 391 TYR 0.008 0.001 TYR A 572 PHE 0.020 0.001 PHE A 319 TRP 0.006 0.001 TRP B 165 HIS 0.009 0.001 HIS B 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 9153) covalent geometry : angle 0.55121 / 0.27 (12374) hydrogen bonds : bond 0.04046 / 2.69 ( 552) hydrogen bonds : angle 3.77566 / 2.77 ( 1626) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.309 Fit side-chains REVERT: A 208 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8301 (tm-30) REVERT: A 212 LYS cc_start: 0.7787 (tttm) cc_final: 0.7161 (ttpt) REVERT: B 210 MET cc_start: 0.9231 (tmm) cc_final: 0.8981 (tmm) REVERT: B 242 MET cc_start: 0.8391 (mmp) cc_final: 0.8141 (mmm) REVERT: B 403 ASP cc_start: 0.7680 (t0) cc_final: 0.7300 (t0) REVERT: B 427 HIS cc_start: 0.6868 (t-90) cc_final: 0.6600 (t-90) outliers start: 22 outliers final: 14 residues processed: 125 average time/residue: 0.0748 time to fit residues: 13.9567 Evaluate side-chains 120 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 551 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 54 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.118639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.105425 restraints weight = 15376.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.108534 restraints weight = 6797.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.110503 restraints weight = 3805.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.111744 restraints weight = 2525.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.112518 restraints weight = 1899.800| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9153 Z= 0.126 Angle : 0.554 8.063 12374 Z= 0.267 Chirality : 0.040 0.141 1466 Planarity : 0.003 0.030 1552 Dihedral : 8.932 127.536 1302 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.86 % Allowed : 12.27 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.26), residues: 1144 helix: 2.11 (0.20), residues: 718 sheet: 0.01 (0.61), residues: 70 loop : -0.94 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 102 TYR 0.008 0.001 TYR A 572 PHE 0.014 0.001 PHE B 265 TRP 0.006 0.001 TRP B 10 HIS 0.009 0.001 HIS B 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 9153) covalent geometry : angle 0.55394 / 0.27 (12374) hydrogen bonds : bond 0.04064 / 2.69 ( 552) hydrogen bonds : angle 3.70340 / 2.71 ( 1626) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.326 Fit side-chains REVERT: A 208 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8096 (tm-30) REVERT: A 212 LYS cc_start: 0.7752 (tttm) cc_final: 0.6936 (mtpt) REVERT: B 210 MET cc_start: 0.9211 (tmm) cc_final: 0.8885 (tmm) REVERT: B 403 ASP cc_start: 0.7695 (t0) cc_final: 0.7365 (t0) REVERT: B 427 HIS cc_start: 0.6849 (t-90) cc_final: 0.6643 (t70) outliers start: 28 outliers final: 18 residues processed: 129 average time/residue: 0.0818 time to fit residues: 15.6146 Evaluate side-chains 125 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 551 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.118635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.105611 restraints weight = 15390.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.108698 restraints weight = 6760.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.110635 restraints weight = 3770.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.111743 restraints weight = 2494.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.112567 restraints weight = 1915.645| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9153 Z= 0.126 Angle : 0.563 9.858 12374 Z= 0.271 Chirality : 0.040 0.150 1466 Planarity : 0.003 0.030 1552 Dihedral : 8.611 126.520 1302 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.25 % Allowed : 13.09 % Favored : 84.66 % 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: 1.63 (0.26), residues: 1144 helix: 2.12 (0.20), residues: 718 sheet: 0.13 (0.62), residues: 70 loop : -0.91 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 102 TYR 0.007 0.001 TYR A 572 PHE 0.014 0.001 PHE A 319 TRP 0.006 0.001 TRP B 10 HIS 0.009 0.001 HIS B 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 9153) covalent geometry : angle 0.56277 / 0.27 (12374) hydrogen bonds : bond 0.04029 / 2.67 ( 552) hydrogen bonds : angle 3.65549 / 2.68 ( 1626) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.329 Fit side-chains REVERT: A 200 MET cc_start: 0.9326 (tpp) cc_final: 0.9082 (tpp) REVERT: A 208 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8089 (tm-30) REVERT: A 212 LYS cc_start: 0.7730 (tttm) cc_final: 0.6864 (mtpt) REVERT: B 210 MET cc_start: 0.9212 (tmm) cc_final: 0.8871 (tmm) REVERT: B 403 ASP cc_start: 0.7682 (t0) cc_final: 0.7360 (t0) REVERT: B 427 HIS cc_start: 0.6804 (t-90) cc_final: 0.6577 (t70) outliers start: 22 outliers final: 17 residues processed: 122 average time/residue: 0.0778 time to fit residues: 13.9540 Evaluate side-chains 124 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 551 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 58 optimal weight: 0.0770 chunk 35 optimal weight: 0.0470 chunk 109 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.120507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.107350 restraints weight = 15227.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.110468 restraints weight = 6732.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.112423 restraints weight = 3765.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.113661 restraints weight = 2496.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.114297 restraints weight = 1878.072| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9153 Z= 0.109 Angle : 0.545 9.993 12374 Z= 0.263 Chirality : 0.039 0.144 1466 Planarity : 0.003 0.031 1552 Dihedral : 8.204 125.512 1302 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.45 % Allowed : 13.09 % Favored : 84.46 % 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: 1.72 (0.26), residues: 1144 helix: 2.12 (0.20), residues: 734 sheet: 0.24 (0.63), residues: 70 loop : -0.88 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 377 TYR 0.007 0.001 TYR A 572 PHE 0.022 0.001 PHE A 288 TRP 0.005 0.001 TRP A 10 HIS 0.010 0.001 HIS B 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 9153) covalent geometry : angle 0.54499 / 0.26 (12374) hydrogen bonds : bond 0.03837 / 2.54 ( 552) hydrogen bonds : angle 3.57443 / 2.61 ( 1626) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.348 Fit side-chains REVERT: A 109 MET cc_start: 0.8575 (tmm) cc_final: 0.8005 (ttp) REVERT: A 196 MET cc_start: 0.7838 (ttt) cc_final: 0.7361 (ttt) REVERT: A 200 MET cc_start: 0.9308 (tpp) cc_final: 0.9057 (tpp) REVERT: A 208 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8122 (tm-30) REVERT: A 212 LYS cc_start: 0.7702 (tttm) cc_final: 0.6873 (mtpt) REVERT: A 535 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8261 (pt) REVERT: B 159 MET cc_start: 0.8749 (tmm) cc_final: 0.8524 (tmm) REVERT: B 210 MET cc_start: 0.9205 (tmm) cc_final: 0.8813 (tmm) REVERT: B 403 ASP cc_start: 0.7644 (t0) cc_final: 0.7324 (t0) REVERT: B 427 HIS cc_start: 0.6700 (t-90) cc_final: 0.6473 (t70) outliers start: 24 outliers final: 18 residues processed: 131 average time/residue: 0.0672 time to fit residues: 13.3519 Evaluate side-chains 132 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 551 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 80 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 43 optimal weight: 0.0470 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 103 optimal weight: 0.0970 chunk 18 optimal weight: 4.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 GLN B 568 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.121835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.108626 restraints weight = 15267.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.111766 restraints weight = 6729.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.113734 restraints weight = 3760.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.114915 restraints weight = 2496.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.115777 restraints weight = 1896.550| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9153 Z= 0.107 Angle : 0.553 9.966 12374 Z= 0.266 Chirality : 0.040 0.138 1466 Planarity : 0.003 0.031 1552 Dihedral : 8.000 124.669 1302 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.04 % Allowed : 14.62 % Favored : 83.33 % 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: 1.75 (0.26), residues: 1144 helix: 2.16 (0.20), residues: 734 sheet: 0.29 (0.63), residues: 70 loop : -0.89 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 102 TYR 0.016 0.001 TYR A 162 PHE 0.016 0.001 PHE A 288 TRP 0.005 0.001 TRP B 17 HIS 0.011 0.001 HIS B 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 ( 9153) covalent geometry : angle 0.55263 / 0.27 (12374) hydrogen bonds : bond 0.03778 / 2.51 ( 552) hydrogen bonds : angle 3.56053 / 2.60 ( 1626) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.236 Fit side-chains REVERT: A 109 MET cc_start: 0.8544 (tmm) cc_final: 0.7943 (ttp) REVERT: A 208 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8117 (tm-30) REVERT: A 212 LYS cc_start: 0.7709 (tttm) cc_final: 0.6930 (mtpt) REVERT: A 535 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8331 (pt) REVERT: B 34 LEU cc_start: 0.8575 (tp) cc_final: 0.8370 (tp) REVERT: B 159 MET cc_start: 0.8743 (tmm) cc_final: 0.8506 (tmm) REVERT: B 210 MET cc_start: 0.9189 (tmm) cc_final: 0.8768 (tmm) REVERT: B 403 ASP cc_start: 0.7642 (t0) cc_final: 0.7322 (t0) REVERT: B 427 HIS cc_start: 0.6598 (t-90) cc_final: 0.6381 (t70) outliers start: 20 outliers final: 13 residues processed: 125 average time/residue: 0.0707 time to fit residues: 13.2117 Evaluate side-chains 125 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 551 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 63 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 0.0170 chunk 27 optimal weight: 0.6980 chunk 32 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 562 HIS B 568 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.122014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.108799 restraints weight = 15277.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.111913 restraints weight = 6766.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.113901 restraints weight = 3787.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.115119 restraints weight = 2498.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.115923 restraints weight = 1885.064| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9153 Z= 0.109 Angle : 0.565 10.471 12374 Z= 0.269 Chirality : 0.040 0.141 1466 Planarity : 0.003 0.032 1552 Dihedral : 7.837 123.366 1302 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.04 % Allowed : 15.13 % Favored : 82.82 % 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: 1.82 (0.26), residues: 1144 helix: 2.21 (0.20), residues: 734 sheet: 0.37 (0.63), residues: 70 loop : -0.90 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 102 TYR 0.014 0.001 TYR A 162 PHE 0.027 0.001 PHE A 288 TRP 0.007 0.001 TRP B 17 HIS 0.013 0.001 HIS B 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 9153) covalent geometry : angle 0.56537 / 0.27 (12374) hydrogen bonds : bond 0.03759 / 2.49 ( 552) hydrogen bonds : angle 3.54742 / 2.58 ( 1626) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.345 Fit side-chains REVERT: A 109 MET cc_start: 0.8559 (tmm) cc_final: 0.7937 (ttp) REVERT: A 208 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8163 (tm-30) REVERT: A 212 LYS cc_start: 0.7715 (tttm) cc_final: 0.6962 (mtpt) REVERT: A 361 ASN cc_start: 0.7750 (p0) cc_final: 0.7447 (p0) REVERT: A 535 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8354 (pt) REVERT: B 34 LEU cc_start: 0.8545 (tp) cc_final: 0.8341 (tp) REVERT: B 159 MET cc_start: 0.8724 (tmm) cc_final: 0.8495 (tmm) REVERT: B 210 MET cc_start: 0.9172 (tmm) cc_final: 0.8764 (tmm) REVERT: B 403 ASP cc_start: 0.7613 (t0) cc_final: 0.7332 (t0) REVERT: B 427 HIS cc_start: 0.6556 (t-90) cc_final: 0.6316 (t70) outliers start: 20 outliers final: 17 residues processed: 125 average time/residue: 0.0713 time to fit residues: 13.4795 Evaluate side-chains 129 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 551 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 27 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 405 HIS B 568 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.120474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.107425 restraints weight = 15299.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.110508 restraints weight = 6741.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.112431 restraints weight = 3773.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.113699 restraints weight = 2505.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.114488 restraints weight = 1870.619| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9153 Z= 0.121 Angle : 0.578 10.113 12374 Z= 0.275 Chirality : 0.040 0.169 1466 Planarity : 0.003 0.032 1552 Dihedral : 7.771 122.231 1302 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.15 % Allowed : 15.64 % Favored : 82.21 % 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: 1.82 (0.26), residues: 1144 helix: 2.22 (0.20), residues: 734 sheet: 0.39 (0.63), residues: 70 loop : -0.93 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 102 TYR 0.018 0.001 TYR B 351 PHE 0.017 0.001 PHE B 265 TRP 0.005 0.001 TRP B 10 HIS 0.015 0.001 HIS B 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 9153) covalent geometry : angle 0.57810 / 0.28 (12374) hydrogen bonds : bond 0.03863 / 2.56 ( 552) hydrogen bonds : angle 3.58759 / 2.61 ( 1626) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.372 Fit side-chains REVERT: A 109 MET cc_start: 0.8618 (tmm) cc_final: 0.8149 (ttp) REVERT: A 208 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8149 (tm-30) REVERT: A 212 LYS cc_start: 0.7715 (tttm) cc_final: 0.6960 (mtpt) REVERT: A 535 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8377 (pt) REVERT: B 34 LEU cc_start: 0.8557 (tp) cc_final: 0.8343 (tp) REVERT: B 237 MET cc_start: 0.8699 (tpt) cc_final: 0.8291 (tpt) REVERT: B 403 ASP cc_start: 0.7677 (t0) cc_final: 0.7367 (t0) REVERT: B 427 HIS cc_start: 0.6733 (t-90) cc_final: 0.6469 (t70) outliers start: 21 outliers final: 18 residues processed: 119 average time/residue: 0.0679 time to fit residues: 12.3245 Evaluate side-chains 128 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 551 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 40 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 62 optimal weight: 0.1980 chunk 112 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 568 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.120868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.107713 restraints weight = 15123.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.110796 restraints weight = 6718.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.112759 restraints weight = 3775.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.114008 restraints weight = 2507.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.114780 restraints weight = 1878.540| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9153 Z= 0.117 Angle : 0.577 10.103 12374 Z= 0.274 Chirality : 0.040 0.147 1466 Planarity : 0.003 0.032 1552 Dihedral : 7.694 120.768 1302 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.94 % Allowed : 16.26 % Favored : 81.80 % 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: 1.83 (0.26), residues: 1144 helix: 2.23 (0.20), residues: 734 sheet: 0.44 (0.64), residues: 70 loop : -0.93 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 102 TYR 0.016 0.001 TYR B 351 PHE 0.025 0.001 PHE A 288 TRP 0.005 0.001 TRP B 10 HIS 0.014 0.001 HIS B 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 9153) covalent geometry : angle 0.57667 / 0.27 (12374) hydrogen bonds : bond 0.03844 / 2.55 ( 552) hydrogen bonds : angle 3.57912 / 2.60 ( 1626) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1235.32 seconds wall clock time: 22 minutes 10.70 seconds (1330.70 seconds total)