Starting phenix.real_space_refine on Fri Jun 6 16:38:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wd6_37455/06_2025/8wd6_37455.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wd6_37455/06_2025/8wd6_37455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wd6_37455/06_2025/8wd6_37455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wd6_37455/06_2025/8wd6_37455.map" model { file = "/net/cci-nas-00/data/ceres_data/8wd6_37455/06_2025/8wd6_37455.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wd6_37455/06_2025/8wd6_37455.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.004 sd= 0.075 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: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 5206 2.51 5 N 1325 2.21 5 O 1390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 7973 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3983 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 17, 'TRANS': 494} Chain breaks: 4 Chain: "B" Number of atoms: 3990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3990 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 17, 'TRANS': 495} Chain breaks: 4 Time building chain proxies: 5.04, per 1000 atoms: 0.63 Number of scatterers: 7973 At special positions: 0 Unit cell: (82.125, 101.835, 127.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1390 8.00 N 1325 7.00 C 5206 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 606 " - pdb=" SG CYS A 622 " distance=2.03 Simple disulfide: pdb=" SG CYS B 606 " - pdb=" SG CYS B 622 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 1.0 seconds 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1878 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 5 sheets defined 68.0% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 106 through 116 removed outlier: 3.690A pdb=" N LEU A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.610A pdb=" N LYS A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 169 Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 208 through 222 removed outlier: 3.918A pdb=" N GLU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 255 removed outlier: 3.538A pdb=" N ALA A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 274 Processing helix chain 'A' and resid 292 through 303 removed outlier: 4.502A pdb=" N MET A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 320 Processing helix chain 'A' and resid 379 through 406 removed outlier: 5.016A pdb=" N LYS A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLU A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.532A pdb=" N PHE A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 455 Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 457 through 462 Processing helix chain 'A' and resid 462 through 472 removed outlier: 3.534A pdb=" N SER A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 492 Processing helix chain 'A' and resid 493 through 508 removed outlier: 4.305A pdb=" N TRP A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N MET A 506 " --> pdb=" O PHE A 502 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR A 508 " --> pdb=" O TYR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 541 removed outlier: 3.824A pdb=" N ILE A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 560 Processing helix chain 'A' and resid 570 through 574 removed outlier: 3.779A pdb=" N VAL A 574 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 579 removed outlier: 3.562A pdb=" N TYR A 578 " --> pdb=" O TRP A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 594 removed outlier: 3.586A pdb=" N TYR A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 removed outlier: 3.514A pdb=" N GLY A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 629 Processing helix chain 'A' and resid 634 through 660 removed outlier: 3.568A pdb=" N SER A 638 " --> pdb=" O GLY A 634 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 639 " --> pdb=" O MET A 635 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 removed outlier: 3.548A pdb=" N LEU B 110 " --> pdb=" O GLY B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 141 removed outlier: 4.144A pdb=" N ARG B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 169 Processing helix chain 'B' and resid 174 through 189 Processing helix chain 'B' and resid 208 through 220 removed outlier: 4.172A pdb=" N GLU B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 255 removed outlier: 3.506A pdb=" N ALA B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 274 removed outlier: 3.591A pdb=" N GLN B 273 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 303 removed outlier: 4.535A pdb=" N ALA B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 320 Processing helix chain 'B' and resid 379 through 406 removed outlier: 5.045A pdb=" N LYS B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N GLU B 400 " --> pdb=" O ARG B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 Processing helix chain 'B' and resid 432 through 455 Proline residue: B 451 - end of helix Processing helix chain 'B' and resid 457 through 462 removed outlier: 3.546A pdb=" N GLU B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 472 Processing helix chain 'B' and resid 476 through 492 Processing helix chain 'B' and resid 493 through 508 removed outlier: 3.503A pdb=" N ALA B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TRP B 505 " --> pdb=" O THR B 501 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N MET B 506 " --> pdb=" O PHE B 502 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR B 508 " --> pdb=" O TYR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 541 removed outlier: 3.780A pdb=" N ILE B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 561 Processing helix chain 'B' and resid 570 through 579 removed outlier: 3.755A pdb=" N VAL B 574 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N TRP B 575 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET B 576 " --> pdb=" O MET B 573 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 577 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 579 " --> pdb=" O MET B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 594 removed outlier: 3.568A pdb=" N TYR B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 604 Processing helix chain 'B' and resid 619 through 630 removed outlier: 3.805A pdb=" N GLU B 628 " --> pdb=" O PHE B 624 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 629 " --> pdb=" O VAL B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 660 removed outlier: 3.657A pdb=" N SER B 638 " --> pdb=" O GLY B 634 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 639 " --> pdb=" O MET B 635 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG B 650 " --> pdb=" O PHE B 646 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 91 removed outlier: 3.645A pdb=" N GLY A 89 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE A 42 " --> pdb=" O GLY A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 261 through 263 removed outlier: 7.171A pdb=" N VAL A 278 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL A 289 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU A 280 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 143 Processing sheet with id=AA4, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.694A pdb=" N LYS B 126 " --> pdb=" O VAL B 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.041A pdb=" N GLY B 143 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU B 228 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N SER B 263 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LEU B 230 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL B 278 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL B 289 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU B 280 " --> pdb=" O LEU B 287 " (cutoff:3.500A) 485 hydrogen bonds defined for protein. 1425 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: 2.12 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2474 1.34 - 1.46: 1890 1.46 - 1.58: 3693 1.58 - 1.70: 0 1.70 - 1.81: 86 Bond restraints: 8143 Sorted by residual: bond pdb=" N VAL A 43 " pdb=" CA VAL A 43 " ideal model delta sigma weight residual 1.457 1.493 -0.037 1.15e-02 7.56e+03 1.01e+01 bond pdb=" N VAL B 43 " pdb=" CA VAL B 43 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.15e-02 7.56e+03 1.00e+01 bond pdb=" N PHE A 459 " pdb=" CA PHE A 459 " ideal model delta sigma weight residual 1.461 1.489 -0.028 9.20e-03 1.18e+04 9.00e+00 bond pdb=" N GLU A 232 " pdb=" CA GLU A 232 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.41e-02 5.03e+03 7.12e+00 bond pdb=" C PHE A 459 " pdb=" N PRO A 460 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.28e-02 6.10e+03 6.67e+00 ... (remaining 8138 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 10808 1.74 - 3.47: 174 3.47 - 5.21: 40 5.21 - 6.95: 6 6.95 - 8.68: 2 Bond angle restraints: 11030 Sorted by residual: angle pdb=" C PHE A 299 " pdb=" CA PHE A 299 " pdb=" CB PHE A 299 " ideal model delta sigma weight residual 110.85 117.56 -6.71 1.70e+00 3.46e-01 1.56e+01 angle pdb=" CA LYS B 140 " pdb=" CB LYS B 140 " pdb=" CG LYS B 140 " ideal model delta sigma weight residual 114.10 120.85 -6.75 2.00e+00 2.50e-01 1.14e+01 angle pdb=" CA PHE A 459 " pdb=" C PHE A 459 " pdb=" O PHE A 459 " ideal model delta sigma weight residual 118.73 115.50 3.23 9.80e-01 1.04e+00 1.08e+01 angle pdb=" CA PHE A 459 " pdb=" C PHE A 459 " pdb=" N PRO A 460 " ideal model delta sigma weight residual 120.77 123.90 -3.13 9.70e-01 1.06e+00 1.04e+01 angle pdb=" CA CYS B 622 " pdb=" C CYS B 622 " pdb=" O CYS B 622 " ideal model delta sigma weight residual 120.42 117.22 3.20 1.06e+00 8.90e-01 9.11e+00 ... (remaining 11025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 4001 16.25 - 32.49: 565 32.49 - 48.74: 179 48.74 - 64.99: 26 64.99 - 81.23: 9 Dihedral angle restraints: 4780 sinusoidal: 1855 harmonic: 2925 Sorted by residual: dihedral pdb=" CB CYS B 606 " pdb=" SG CYS B 606 " pdb=" SG CYS B 622 " pdb=" CB CYS B 622 " ideal model delta sinusoidal sigma weight residual 93.00 135.71 -42.71 1 1.00e+01 1.00e-02 2.55e+01 dihedral pdb=" C PHE A 299 " pdb=" N PHE A 299 " pdb=" CA PHE A 299 " pdb=" CB PHE A 299 " ideal model delta harmonic sigma weight residual -122.60 -132.61 10.01 0 2.50e+00 1.60e-01 1.60e+01 dihedral pdb=" CG ARG B 214 " pdb=" CD ARG B 214 " pdb=" NE ARG B 214 " pdb=" CZ ARG B 214 " ideal model delta sinusoidal sigma weight residual 90.00 134.54 -44.54 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 4777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1122 0.055 - 0.109: 159 0.109 - 0.164: 21 0.164 - 0.219: 2 0.219 - 0.273: 2 Chirality restraints: 1306 Sorted by residual: chirality pdb=" CA PHE A 299 " pdb=" N PHE A 299 " pdb=" C PHE A 299 " pdb=" CB PHE A 299 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB VAL B 43 " pdb=" CA VAL B 43 " pdb=" CG1 VAL B 43 " pdb=" CG2 VAL B 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB VAL A 43 " pdb=" CA VAL A 43 " pdb=" CG1 VAL A 43 " pdb=" CG2 VAL A 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1303 not shown) Planarity restraints: 1351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 598 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.26e+00 pdb=" CD GLU B 598 " 0.047 2.00e-02 2.50e+03 pdb=" OE1 GLU B 598 " -0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU B 598 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 463 " 0.226 9.50e-02 1.11e+02 1.01e-01 6.45e+00 pdb=" NE ARG B 463 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B 463 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 463 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 463 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 314 " -0.010 2.00e-02 2.50e+03 2.14e-02 4.58e+00 pdb=" CG ASP A 314 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASP A 314 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP A 314 " -0.013 2.00e-02 2.50e+03 ... (remaining 1348 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 3277 2.93 - 3.42: 7771 3.42 - 3.91: 12625 3.91 - 4.41: 13867 4.41 - 4.90: 24153 Nonbonded interactions: 61693 Sorted by model distance: nonbonded pdb=" O LEU A 409 " pdb=" NE2 GLN A 413 " model vdw 2.431 3.120 nonbonded pdb=" O GLU A 183 " pdb=" OE1 GLU A 183 " model vdw 2.436 3.040 nonbonded pdb=" OG SER B 405 " pdb=" OE2 GLU B 492 " model vdw 2.439 3.040 nonbonded pdb=" O ARG A 141 " pdb=" N SER A 226 " model vdw 2.452 3.120 nonbonded pdb=" O GLN A 137 " pdb=" NZ LYS A 140 " model vdw 2.453 3.120 ... (remaining 61688 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' selection = (chain 'B' and (resid 35 through 119 or resid 125 through 660)) } 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: 13.570 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.830 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 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 : 0.003 0.049 8145 Z= 0.174 Angle : 0.563 8.682 11034 Z= 0.309 Chirality : 0.040 0.273 1306 Planarity : 0.005 0.101 1351 Dihedral : 16.494 81.232 2896 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.12 % Allowed : 31.10 % Favored : 68.79 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.27), residues: 1005 helix: 1.98 (0.21), residues: 649 sheet: 0.04 (0.72), residues: 70 loop : -0.83 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 447 HIS 0.004 0.001 HIS B 395 PHE 0.026 0.001 PHE B 36 TYR 0.007 0.001 TYR B 480 ARG 0.007 0.001 ARG B 463 Details of bonding type rmsd hydrogen bonds : bond 0.13691 ( 485) hydrogen bonds : angle 4.44847 ( 1425) SS BOND : bond 0.00170 ( 2) SS BOND : angle 0.55800 ( 4) covalent geometry : bond 0.00297 ( 8143) covalent geometry : angle 0.56318 (11030) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7660 (mttt) cc_final: 0.7426 (tptt) REVERT: A 568 LYS cc_start: 0.7780 (mmtt) cc_final: 0.7227 (tmmt) REVERT: B 41 LYS cc_start: 0.8245 (tttt) cc_final: 0.7792 (ttmt) REVERT: B 291 LYS cc_start: 0.6949 (tttt) cc_final: 0.6312 (ttmm) REVERT: B 568 LYS cc_start: 0.7686 (mmtt) cc_final: 0.7207 (tmmt) REVERT: B 576 MET cc_start: 0.8152 (ttm) cc_final: 0.7904 (mtm) outliers start: 1 outliers final: 1 residues processed: 145 average time/residue: 1.2936 time to fit residues: 198.5288 Evaluate side-chains 126 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 660 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.0980 chunk 77 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.165895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.123274 restraints weight = 9510.981| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.02 r_work: 0.3328 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8145 Z= 0.128 Angle : 0.510 6.784 11034 Z= 0.260 Chirality : 0.039 0.132 1306 Planarity : 0.004 0.031 1351 Dihedral : 3.765 26.362 1107 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.86 % Allowed : 29.36 % Favored : 65.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.28), residues: 1005 helix: 2.06 (0.21), residues: 655 sheet: 0.01 (0.65), residues: 75 loop : -0.57 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 426 HIS 0.004 0.001 HIS B 219 PHE 0.015 0.002 PHE A 624 TYR 0.010 0.001 TYR B 430 ARG 0.004 0.000 ARG A 141 Details of bonding type rmsd hydrogen bonds : bond 0.04807 ( 485) hydrogen bonds : angle 3.45566 ( 1425) SS BOND : bond 0.00239 ( 2) SS BOND : angle 0.27174 ( 4) covalent geometry : bond 0.00298 ( 8143) covalent geometry : angle 0.51034 (11030) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7983 (mttt) cc_final: 0.7522 (tppt) REVERT: A 568 LYS cc_start: 0.8171 (mmtt) cc_final: 0.7396 (tmmt) REVERT: A 658 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7452 (ttp-110) REVERT: B 41 LYS cc_start: 0.8053 (tttt) cc_final: 0.7458 (ttmt) REVERT: B 168 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.6624 (ptm160) REVERT: B 291 LYS cc_start: 0.7092 (tttt) cc_final: 0.6300 (ttmm) REVERT: B 568 LYS cc_start: 0.8036 (mmtt) cc_final: 0.7355 (tmmt) outliers start: 42 outliers final: 15 residues processed: 169 average time/residue: 1.4508 time to fit residues: 261.8219 Evaluate side-chains 143 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 632 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 34 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 73 optimal weight: 0.0870 chunk 7 optimal weight: 0.1980 chunk 60 optimal weight: 0.9980 chunk 9 optimal weight: 0.0040 chunk 89 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 overall best weight: 0.4570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN B 265 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.167801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.125747 restraints weight = 9675.203| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.07 r_work: 0.3374 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8145 Z= 0.100 Angle : 0.480 7.231 11034 Z= 0.240 Chirality : 0.037 0.123 1306 Planarity : 0.003 0.029 1351 Dihedral : 3.497 13.943 1105 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.35 % Allowed : 31.56 % Favored : 65.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.28), residues: 1005 helix: 2.15 (0.21), residues: 663 sheet: -0.15 (0.63), residues: 76 loop : -0.69 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 386 HIS 0.002 0.001 HIS B 484 PHE 0.014 0.001 PHE A 624 TYR 0.011 0.001 TYR B 430 ARG 0.005 0.000 ARG A 141 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 485) hydrogen bonds : angle 3.27348 ( 1425) SS BOND : bond 0.00101 ( 2) SS BOND : angle 0.23112 ( 4) covalent geometry : bond 0.00218 ( 8143) covalent geometry : angle 0.48032 (11030) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7965 (mttt) cc_final: 0.7492 (tppt) REVERT: A 568 LYS cc_start: 0.8184 (mmtt) cc_final: 0.7418 (tmmt) REVERT: A 602 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7325 (ppt-90) REVERT: B 41 LYS cc_start: 0.7945 (tttt) cc_final: 0.7380 (ttmt) REVERT: B 291 LYS cc_start: 0.6967 (tttt) cc_final: 0.6171 (ttmm) REVERT: B 568 LYS cc_start: 0.8038 (mmtt) cc_final: 0.7336 (tmmt) REVERT: B 576 MET cc_start: 0.8328 (mtp) cc_final: 0.8062 (mtm) REVERT: B 655 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8168 (mt) outliers start: 29 outliers final: 10 residues processed: 159 average time/residue: 1.1919 time to fit residues: 200.8377 Evaluate side-chains 141 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 655 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 40 optimal weight: 0.3980 chunk 87 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS B 266 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.160440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.117275 restraints weight = 9727.052| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.09 r_work: 0.3244 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 8145 Z= 0.252 Angle : 0.649 7.682 11034 Z= 0.329 Chirality : 0.044 0.162 1306 Planarity : 0.004 0.032 1351 Dihedral : 4.029 16.972 1105 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 5.90 % Allowed : 29.02 % Favored : 65.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.27), residues: 1005 helix: 1.52 (0.20), residues: 656 sheet: -0.17 (0.60), residues: 82 loop : -0.79 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 426 HIS 0.006 0.001 HIS B 219 PHE 0.015 0.002 PHE B 275 TYR 0.012 0.002 TYR B 526 ARG 0.006 0.001 ARG B 436 Details of bonding type rmsd hydrogen bonds : bond 0.06479 ( 485) hydrogen bonds : angle 3.71350 ( 1425) SS BOND : bond 0.00518 ( 2) SS BOND : angle 0.61348 ( 4) covalent geometry : bond 0.00623 ( 8143) covalent geometry : angle 0.64855 (11030) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 129 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 568 LYS cc_start: 0.8261 (mmtt) cc_final: 0.7469 (tmmt) REVERT: A 602 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7234 (ppt-90) REVERT: A 658 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7866 (ttp-110) REVERT: B 41 LYS cc_start: 0.7795 (tttt) cc_final: 0.7066 (ttmt) REVERT: B 291 LYS cc_start: 0.7255 (tttt) cc_final: 0.6339 (ttmm) REVERT: B 394 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7793 (mp) REVERT: B 568 LYS cc_start: 0.8214 (mmtt) cc_final: 0.7452 (tmmt) REVERT: B 576 MET cc_start: 0.8594 (mtp) cc_final: 0.7860 (tpp) outliers start: 51 outliers final: 25 residues processed: 169 average time/residue: 1.1017 time to fit residues: 198.2675 Evaluate side-chains 155 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 658 ARG Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 632 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 14 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 56 optimal weight: 0.0870 chunk 65 optimal weight: 0.4980 chunk 101 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.165428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.123181 restraints weight = 9518.974| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.01 r_work: 0.3340 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8145 Z= 0.105 Angle : 0.502 7.759 11034 Z= 0.252 Chirality : 0.038 0.128 1306 Planarity : 0.003 0.029 1351 Dihedral : 3.615 14.307 1105 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.35 % Allowed : 31.56 % Favored : 65.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.28), residues: 1005 helix: 1.91 (0.21), residues: 665 sheet: -0.37 (0.61), residues: 83 loop : -0.79 (0.40), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 386 HIS 0.002 0.001 HIS B 484 PHE 0.016 0.001 PHE A 624 TYR 0.012 0.001 TYR B 430 ARG 0.006 0.000 ARG A 141 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 485) hydrogen bonds : angle 3.29330 ( 1425) SS BOND : bond 0.00160 ( 2) SS BOND : angle 0.28544 ( 4) covalent geometry : bond 0.00233 ( 8143) covalent geometry : angle 0.50192 (11030) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.871 Fit side-chains REVERT: A 41 LYS cc_start: 0.7874 (mttt) cc_final: 0.7606 (tttt) REVERT: A 409 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7930 (mp) REVERT: A 568 LYS cc_start: 0.8228 (mmtt) cc_final: 0.7430 (tmmt) REVERT: A 602 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7289 (ppt-90) REVERT: B 41 LYS cc_start: 0.7798 (tttt) cc_final: 0.7069 (ttmt) REVERT: B 168 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.6534 (ptm160) REVERT: B 291 LYS cc_start: 0.7103 (tttt) cc_final: 0.6166 (ttmm) REVERT: B 463 ARG cc_start: 0.6487 (tpt170) cc_final: 0.6254 (tpt170) REVERT: B 568 LYS cc_start: 0.8146 (mmtt) cc_final: 0.7428 (tmmt) REVERT: B 576 MET cc_start: 0.8388 (mtp) cc_final: 0.7829 (tpp) outliers start: 29 outliers final: 10 residues processed: 154 average time/residue: 1.1853 time to fit residues: 193.6663 Evaluate side-chains 138 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 449 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 3 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS B 266 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.160100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.117310 restraints weight = 9630.953| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.07 r_work: 0.3248 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 8145 Z= 0.240 Angle : 0.648 8.559 11034 Z= 0.326 Chirality : 0.043 0.162 1306 Planarity : 0.004 0.041 1351 Dihedral : 4.006 16.605 1105 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 5.32 % Allowed : 29.83 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.27), residues: 1005 helix: 1.47 (0.20), residues: 656 sheet: -0.46 (0.60), residues: 78 loop : -0.83 (0.40), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 426 HIS 0.005 0.001 HIS B 219 PHE 0.015 0.002 PHE A 624 TYR 0.011 0.002 TYR A 526 ARG 0.005 0.001 ARG B 436 Details of bonding type rmsd hydrogen bonds : bond 0.06231 ( 485) hydrogen bonds : angle 3.66647 ( 1425) SS BOND : bond 0.00431 ( 2) SS BOND : angle 0.69049 ( 4) covalent geometry : bond 0.00592 ( 8143) covalent geometry : angle 0.64823 (11030) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 131 time to evaluate : 0.839 Fit side-chains REVERT: A 394 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7823 (mp) REVERT: A 568 LYS cc_start: 0.8294 (mmtt) cc_final: 0.7455 (tmmt) REVERT: A 602 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7312 (ppt-90) REVERT: A 655 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8040 (tp) REVERT: B 41 LYS cc_start: 0.7752 (tttt) cc_final: 0.6955 (ttmt) REVERT: B 394 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7821 (mp) REVERT: B 463 ARG cc_start: 0.6645 (tpt170) cc_final: 0.6392 (tpt170) REVERT: B 568 LYS cc_start: 0.8256 (mmtt) cc_final: 0.7479 (tmmt) outliers start: 46 outliers final: 25 residues processed: 167 average time/residue: 1.0738 time to fit residues: 191.0556 Evaluate side-chains 147 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 632 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 11 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS B 266 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.161758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.118927 restraints weight = 9702.188| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.07 r_work: 0.3283 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8145 Z= 0.172 Angle : 0.587 8.503 11034 Z= 0.298 Chirality : 0.041 0.138 1306 Planarity : 0.004 0.038 1351 Dihedral : 3.897 16.150 1105 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.51 % Allowed : 31.45 % Favored : 64.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.28), residues: 1005 helix: 1.59 (0.21), residues: 657 sheet: -1.04 (0.61), residues: 77 loop : -0.70 (0.40), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 426 HIS 0.004 0.001 HIS B 219 PHE 0.016 0.002 PHE A 624 TYR 0.009 0.002 TYR A 526 ARG 0.006 0.000 ARG A 141 Details of bonding type rmsd hydrogen bonds : bond 0.05199 ( 485) hydrogen bonds : angle 3.52691 ( 1425) SS BOND : bond 0.00325 ( 2) SS BOND : angle 0.52859 ( 4) covalent geometry : bond 0.00422 ( 8143) covalent geometry : angle 0.58728 (11030) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 122 time to evaluate : 0.932 Fit side-chains REVERT: A 41 LYS cc_start: 0.7950 (tttt) cc_final: 0.7733 (ttmt) REVERT: A 188 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7558 (mp0) REVERT: A 394 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7839 (mp) REVERT: A 568 LYS cc_start: 0.8391 (mmtt) cc_final: 0.7497 (tmmt) REVERT: A 602 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7241 (ppt-90) REVERT: B 41 LYS cc_start: 0.7766 (tttt) cc_final: 0.6945 (ttmt) REVERT: B 394 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7836 (mp) REVERT: B 541 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7598 (pp) REVERT: B 568 LYS cc_start: 0.8255 (mmtt) cc_final: 0.7446 (tmmt) REVERT: B 576 MET cc_start: 0.8619 (mtp) cc_final: 0.7940 (tpp) outliers start: 39 outliers final: 21 residues processed: 147 average time/residue: 1.0822 time to fit residues: 169.8423 Evaluate side-chains 145 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 632 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 84 optimal weight: 0.9980 chunk 70 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.164065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.121324 restraints weight = 9643.937| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.08 r_work: 0.3319 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8145 Z= 0.118 Angle : 0.551 8.532 11034 Z= 0.272 Chirality : 0.039 0.144 1306 Planarity : 0.003 0.036 1351 Dihedral : 3.698 15.357 1105 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.05 % Allowed : 31.33 % Favored : 64.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.28), residues: 1005 helix: 1.84 (0.21), residues: 658 sheet: -0.88 (0.62), residues: 77 loop : -0.69 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 425 HIS 0.003 0.001 HIS B 484 PHE 0.016 0.001 PHE A 624 TYR 0.012 0.001 TYR B 430 ARG 0.007 0.000 ARG A 141 Details of bonding type rmsd hydrogen bonds : bond 0.04147 ( 485) hydrogen bonds : angle 3.35036 ( 1425) SS BOND : bond 0.00211 ( 2) SS BOND : angle 0.33546 ( 4) covalent geometry : bond 0.00270 ( 8143) covalent geometry : angle 0.55122 (11030) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8288 (tt) cc_final: 0.8008 (tp) REVERT: A 141 ARG cc_start: 0.7236 (mtt-85) cc_final: 0.6969 (mtp85) REVERT: A 409 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7931 (mp) REVERT: A 568 LYS cc_start: 0.8401 (mmtt) cc_final: 0.7483 (tmmt) REVERT: A 602 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7215 (ppt-90) REVERT: A 655 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8002 (tp) REVERT: B 41 LYS cc_start: 0.7749 (tttt) cc_final: 0.6963 (ttmt) REVERT: B 506 MET cc_start: 0.8229 (ttm) cc_final: 0.7850 (mtp) REVERT: B 568 LYS cc_start: 0.8242 (mmtt) cc_final: 0.7399 (tmmt) REVERT: B 576 MET cc_start: 0.8469 (mtp) cc_final: 0.7828 (tpp) outliers start: 35 outliers final: 18 residues processed: 149 average time/residue: 1.1250 time to fit residues: 178.3458 Evaluate side-chains 140 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 632 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 63 optimal weight: 0.0570 chunk 4 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.163891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.121105 restraints weight = 9770.803| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.09 r_work: 0.3310 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8145 Z= 0.127 Angle : 0.560 8.546 11034 Z= 0.281 Chirality : 0.039 0.130 1306 Planarity : 0.004 0.033 1351 Dihedral : 3.658 15.389 1105 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.82 % Allowed : 31.79 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.28), residues: 1005 helix: 1.89 (0.21), residues: 653 sheet: -0.83 (0.62), residues: 77 loop : -0.70 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 425 HIS 0.003 0.001 HIS A 219 PHE 0.016 0.001 PHE B 304 TYR 0.010 0.001 TYR B 430 ARG 0.006 0.000 ARG A 141 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 485) hydrogen bonds : angle 3.32517 ( 1425) SS BOND : bond 0.00208 ( 2) SS BOND : angle 0.36030 ( 4) covalent geometry : bond 0.00298 ( 8143) covalent geometry : angle 0.56028 (11030) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.885 Fit side-chains REVERT: A 40 LEU cc_start: 0.8266 (tt) cc_final: 0.7993 (tp) REVERT: A 141 ARG cc_start: 0.7251 (mtt-85) cc_final: 0.6981 (mtp85) REVERT: A 409 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7914 (mp) REVERT: A 568 LYS cc_start: 0.8415 (mmtt) cc_final: 0.7483 (tmmt) REVERT: A 602 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7310 (ppt-90) REVERT: A 655 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8026 (tp) REVERT: B 41 LYS cc_start: 0.7739 (tttt) cc_final: 0.7172 (ttmt) REVERT: B 90 MET cc_start: 0.7673 (ttt) cc_final: 0.7248 (ttp) REVERT: B 506 MET cc_start: 0.8259 (ttm) cc_final: 0.7875 (mtp) REVERT: B 568 LYS cc_start: 0.8341 (mmtt) cc_final: 0.7475 (tmmt) REVERT: B 576 MET cc_start: 0.8487 (mtp) cc_final: 0.7840 (tpp) REVERT: B 598 GLU cc_start: 0.7917 (pp20) cc_final: 0.7290 (mm-30) outliers start: 33 outliers final: 19 residues processed: 147 average time/residue: 1.4546 time to fit residues: 227.3036 Evaluate side-chains 143 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 632 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 36 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.164776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.122345 restraints weight = 9631.303| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.03 r_work: 0.3315 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8145 Z= 0.117 Angle : 0.556 8.681 11034 Z= 0.275 Chirality : 0.038 0.126 1306 Planarity : 0.003 0.032 1351 Dihedral : 3.586 14.877 1105 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.54 % Allowed : 32.83 % Favored : 64.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.28), residues: 1005 helix: 2.01 (0.21), residues: 647 sheet: -0.78 (0.61), residues: 78 loop : -0.60 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 425 HIS 0.002 0.001 HIS B 484 PHE 0.015 0.001 PHE A 304 TYR 0.011 0.001 TYR B 430 ARG 0.007 0.000 ARG B 658 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 485) hydrogen bonds : angle 3.27141 ( 1425) SS BOND : bond 0.00169 ( 2) SS BOND : angle 0.30037 ( 4) covalent geometry : bond 0.00273 ( 8143) covalent geometry : angle 0.55581 (11030) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.854 Fit side-chains REVERT: A 40 LEU cc_start: 0.8277 (tt) cc_final: 0.7968 (tp) REVERT: A 141 ARG cc_start: 0.7293 (mtt-85) cc_final: 0.7020 (mtp85) REVERT: A 409 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7936 (mp) REVERT: A 568 LYS cc_start: 0.8368 (mmtt) cc_final: 0.7495 (tmmt) REVERT: A 602 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7304 (ppt-90) REVERT: A 655 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8051 (tp) REVERT: B 41 LYS cc_start: 0.7755 (tttt) cc_final: 0.7192 (ttmt) REVERT: B 90 MET cc_start: 0.7722 (ttt) cc_final: 0.7261 (ttp) REVERT: B 506 MET cc_start: 0.8241 (ttm) cc_final: 0.7871 (mtp) REVERT: B 568 LYS cc_start: 0.8336 (mmtt) cc_final: 0.7484 (tmmt) REVERT: B 576 MET cc_start: 0.8469 (mtp) cc_final: 0.7856 (tpp) outliers start: 22 outliers final: 18 residues processed: 141 average time/residue: 1.1076 time to fit residues: 166.1542 Evaluate side-chains 138 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 632 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 82 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 22 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.162946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.120114 restraints weight = 9703.644| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.08 r_work: 0.3308 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8145 Z= 0.150 Angle : 0.586 8.734 11034 Z= 0.294 Chirality : 0.040 0.131 1306 Planarity : 0.004 0.043 1351 Dihedral : 3.728 17.790 1105 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.58 % Allowed : 32.02 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.28), residues: 1005 helix: 1.90 (0.21), residues: 647 sheet: -0.86 (0.61), residues: 78 loop : -0.59 (0.40), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 426 HIS 0.003 0.001 HIS B 219 PHE 0.016 0.002 PHE B 304 TYR 0.009 0.001 TYR B 430 ARG 0.008 0.001 ARG B 658 Details of bonding type rmsd hydrogen bonds : bond 0.04631 ( 485) hydrogen bonds : angle 3.36898 ( 1425) SS BOND : bond 0.00223 ( 2) SS BOND : angle 0.43500 ( 4) covalent geometry : bond 0.00364 ( 8143) covalent geometry : angle 0.58582 (11030) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6796.09 seconds wall clock time: 118 minutes 37.52 seconds (7117.52 seconds total)