Starting phenix.real_space_refine on Wed Sep 25 03:15:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvc_4647/09_2024/6qvc_4647.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvc_4647/09_2024/6qvc_4647.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvc_4647/09_2024/6qvc_4647.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvc_4647/09_2024/6qvc_4647.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvc_4647/09_2024/6qvc_4647.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qvc_4647/09_2024/6qvc_4647.cif" } resolution = 4.0 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= 0.000 sd= 0.003 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 70 5.16 5 C 6132 2.51 5 N 1484 2.21 5 O 1586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9272 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4636 Classifications: {'peptide': 599} Link IDs: {'CIS': 1, 'PTRANS': 28, 'TRANS': 569} Chain breaks: 3 Restraints were copied for chains: B Time building chain proxies: 8.74, per 1000 atoms: 0.94 Number of scatterers: 9272 At special positions: 0 Unit cell: (105.93, 103.79, 109.14, 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 70 16.00 O 1586 8.00 N 1484 7.00 C 6132 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: 2.19 Conformation dependent library (CDL) restraints added in 1.3 seconds 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2216 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 6 sheets defined 66.4% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'B' and resid 116 through 153 Processing helix chain 'B' and resid 158 through 181 Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 190 through 199 removed outlier: 4.413A pdb=" N MET B 194 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 207 Processing helix chain 'B' and resid 208 through 225 removed outlier: 3.627A pdb=" N PHE B 212 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 213 " --> pdb=" O MET B 209 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL B 217 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 250 removed outlier: 3.611A pdb=" N PHE B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 280 Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 298 through 324 removed outlier: 3.549A pdb=" N ARG B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 320 " --> pdb=" O PHE B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 377 removed outlier: 4.151A pdb=" N CYS B 358 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY B 375 " --> pdb=" O GLN B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 389 Processing helix chain 'B' and resid 391 through 403 removed outlier: 4.691A pdb=" N GLY B 395 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL B 397 " --> pdb=" O TYR B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 428 Processing helix chain 'B' and resid 444 through 450 removed outlier: 3.516A pdb=" N ILE B 450 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 477 removed outlier: 3.530A pdb=" N ILE B 459 " --> pdb=" O ASN B 455 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE B 472 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL B 473 " --> pdb=" O TRP B 469 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET B 477 " --> pdb=" O VAL B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 506 Processing helix chain 'B' and resid 521 through 538 removed outlier: 4.539A pdb=" N THR B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 551 removed outlier: 3.948A pdb=" N VAL B 544 " --> pdb=" O VAL B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 574 Processing helix chain 'B' and resid 576 through 586 Processing helix chain 'B' and resid 621 through 632 Processing helix chain 'B' and resid 654 through 666 Processing helix chain 'B' and resid 833 through 845 Processing helix chain 'B' and resid 862 through 871 Processing helix chain 'A' and resid 116 through 153 Processing helix chain 'A' and resid 158 through 181 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 190 through 199 removed outlier: 4.413A pdb=" N MET A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 208 through 225 removed outlier: 3.626A pdb=" N PHE A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL A 217 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 250 removed outlier: 3.610A pdb=" N PHE A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 280 Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 298 through 324 removed outlier: 3.550A pdb=" N ARG A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 377 removed outlier: 4.151A pdb=" N CYS A 358 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY A 375 " --> pdb=" O GLN A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 389 Processing helix chain 'A' and resid 391 through 403 removed outlier: 4.691A pdb=" N GLY A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL A 397 " --> pdb=" O TYR A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 428 Processing helix chain 'A' and resid 444 through 450 removed outlier: 3.516A pdb=" N ILE A 450 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 477 removed outlier: 3.530A pdb=" N ILE A 459 " --> pdb=" O ASN A 455 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE A 472 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL A 473 " --> pdb=" O TRP A 469 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET A 477 " --> pdb=" O VAL A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 506 Processing helix chain 'A' and resid 521 through 538 removed outlier: 4.538A pdb=" N THR A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 551 removed outlier: 3.949A pdb=" N VAL A 544 " --> pdb=" O VAL A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 574 Processing helix chain 'A' and resid 576 through 586 Processing helix chain 'A' and resid 621 through 632 Processing helix chain 'A' and resid 654 through 666 Processing helix chain 'A' and resid 833 through 845 Processing helix chain 'A' and resid 862 through 871 Processing sheet with id=AA1, first strand: chain 'B' and resid 510 through 512 Processing sheet with id=AA2, first strand: chain 'B' and resid 616 through 617 removed outlier: 6.096A pdb=" N VAL B 616 " --> pdb=" O VAL B 640 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP B 822 " --> pdb=" O SER B 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 849 through 853 removed outlier: 6.582A pdb=" N ALA B 849 " --> pdb=" O VAL B 860 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL B 860 " --> pdb=" O ALA B 849 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL B 851 " --> pdb=" O ARG B 858 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 510 through 512 Processing sheet with id=AA5, first strand: chain 'A' and resid 616 through 617 removed outlier: 6.096A pdb=" N VAL A 616 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP A 822 " --> pdb=" O SER A 651 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 849 through 853 removed outlier: 6.581A pdb=" N ALA A 849 " --> pdb=" O VAL A 860 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL A 860 " --> pdb=" O ALA A 849 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL A 851 " --> pdb=" O ARG A 858 " (cutoff:3.500A) 586 hydrogen bonds defined for protein. 1710 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: 2.70 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2748 1.34 - 1.46: 2200 1.46 - 1.58: 4440 1.58 - 1.70: 0 1.70 - 1.82: 116 Bond restraints: 9504 Sorted by residual: bond pdb=" CG1 ILE B 527 " pdb=" CD1 ILE B 527 " ideal model delta sigma weight residual 1.513 1.389 0.124 3.90e-02 6.57e+02 1.02e+01 bond pdb=" CG1 ILE A 527 " pdb=" CD1 ILE A 527 " ideal model delta sigma weight residual 1.513 1.389 0.124 3.90e-02 6.57e+02 1.01e+01 bond pdb=" CB ILE A 354 " pdb=" CG2 ILE A 354 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.68e+00 bond pdb=" CB ILE B 354 " pdb=" CG2 ILE B 354 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.63e+00 bond pdb=" C PHE A 343 " pdb=" N ASP A 344 " ideal model delta sigma weight residual 1.329 1.362 -0.033 1.40e-02 5.10e+03 5.68e+00 ... (remaining 9499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.15: 12606 4.15 - 8.29: 262 8.29 - 12.44: 36 12.44 - 16.59: 8 16.59 - 20.73: 2 Bond angle restraints: 12914 Sorted by residual: angle pdb=" C PHE A 343 " pdb=" N ASP A 344 " pdb=" CA ASP A 344 " ideal model delta sigma weight residual 121.70 132.56 -10.86 1.80e+00 3.09e-01 3.64e+01 angle pdb=" C PHE B 343 " pdb=" N ASP B 344 " pdb=" CA ASP B 344 " ideal model delta sigma weight residual 121.70 132.48 -10.78 1.80e+00 3.09e-01 3.59e+01 angle pdb=" CA LEU A 171 " pdb=" CB LEU A 171 " pdb=" CG LEU A 171 " ideal model delta sigma weight residual 116.30 137.03 -20.73 3.50e+00 8.16e-02 3.51e+01 angle pdb=" CA LEU B 171 " pdb=" CB LEU B 171 " pdb=" CG LEU B 171 " ideal model delta sigma weight residual 116.30 136.99 -20.69 3.50e+00 8.16e-02 3.49e+01 angle pdb=" C THR B 621 " pdb=" N TYR B 622 " pdb=" CA TYR B 622 " ideal model delta sigma weight residual 120.82 128.30 -7.48 1.50e+00 4.44e-01 2.49e+01 ... (remaining 12909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.08: 4989 14.08 - 28.16: 433 28.16 - 42.24: 108 42.24 - 56.32: 20 56.32 - 70.40: 6 Dihedral angle restraints: 5556 sinusoidal: 2114 harmonic: 3442 Sorted by residual: dihedral pdb=" CA ALA A 326 " pdb=" C ALA A 326 " pdb=" N VAL A 327 " pdb=" CA VAL A 327 " ideal model delta harmonic sigma weight residual 180.00 -135.06 -44.94 0 5.00e+00 4.00e-02 8.08e+01 dihedral pdb=" CA ALA B 326 " pdb=" C ALA B 326 " pdb=" N VAL B 327 " pdb=" CA VAL B 327 " ideal model delta harmonic sigma weight residual 180.00 -135.14 -44.86 0 5.00e+00 4.00e-02 8.05e+01 dihedral pdb=" CA ILE B 290 " pdb=" C ILE B 290 " pdb=" N GLU B 291 " pdb=" CA GLU B 291 " ideal model delta harmonic sigma weight residual -180.00 -145.15 -34.85 0 5.00e+00 4.00e-02 4.86e+01 ... (remaining 5553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1322 0.112 - 0.225: 171 0.225 - 0.337: 31 0.337 - 0.450: 0 0.450 - 0.562: 2 Chirality restraints: 1526 Sorted by residual: chirality pdb=" CB VAL B 321 " pdb=" CA VAL B 321 " pdb=" CG1 VAL B 321 " pdb=" CG2 VAL B 321 " both_signs ideal model delta sigma weight residual False -2.63 -2.07 -0.56 2.00e-01 2.50e+01 7.90e+00 chirality pdb=" CB VAL A 321 " pdb=" CA VAL A 321 " pdb=" CG1 VAL A 321 " pdb=" CG2 VAL A 321 " both_signs ideal model delta sigma weight residual False -2.63 -2.07 -0.56 2.00e-01 2.50e+01 7.84e+00 chirality pdb=" CB ILE B 329 " pdb=" CA ILE B 329 " pdb=" CG1 ILE B 329 " pdb=" CG2 ILE B 329 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 1523 not shown) Planarity restraints: 1580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 469 " 0.035 2.00e-02 2.50e+03 2.09e-02 1.09e+01 pdb=" CG TRP B 469 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP B 469 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP B 469 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP B 469 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 469 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 469 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 469 " 0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 469 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 469 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 469 " -0.035 2.00e-02 2.50e+03 2.09e-02 1.09e+01 pdb=" CG TRP A 469 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP A 469 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 469 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 469 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 469 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 469 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 469 " -0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 469 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 469 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 327 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C VAL A 327 " -0.056 2.00e-02 2.50e+03 pdb=" O VAL A 327 " 0.021 2.00e-02 2.50e+03 pdb=" N THR A 328 " 0.019 2.00e-02 2.50e+03 ... (remaining 1577 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1622 2.77 - 3.30: 9375 3.30 - 3.83: 15743 3.83 - 4.37: 17403 4.37 - 4.90: 28449 Nonbonded interactions: 72592 Sorted by model distance: nonbonded pdb=" O ILE A 472 " pdb=" OG1 THR A 476 " model vdw 2.232 3.040 nonbonded pdb=" O ILE B 472 " pdb=" OG1 THR B 476 " model vdw 2.232 3.040 nonbonded pdb=" O ILE B 401 " pdb=" OG1 THR B 405 " model vdw 2.237 3.040 nonbonded pdb=" O ILE A 401 " pdb=" OG1 THR A 405 " model vdw 2.237 3.040 nonbonded pdb=" OG1 THR B 632 " pdb=" NH1 ARG B 654 " model vdw 2.249 3.120 ... (remaining 72587 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' } 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: 1.040 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: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.560 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 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 : 0.008 0.124 9504 Z= 0.520 Angle : 1.474 20.735 12914 Z= 0.771 Chirality : 0.080 0.562 1526 Planarity : 0.010 0.059 1580 Dihedral : 11.978 70.398 3340 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.38 % Favored : 91.12 % Rotamer: Outliers : 2.19 % Allowed : 8.95 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.71 % 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: -3.90 (0.20), residues: 1182 helix: -2.23 (0.15), residues: 758 sheet: -0.42 (0.90), residues: 20 loop : -3.15 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.005 TRP A 469 HIS 0.008 0.002 HIS A 835 PHE 0.037 0.004 PHE A 547 TYR 0.031 0.003 TYR B 589 ARG 0.008 0.001 ARG A 626 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 225 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 LEU cc_start: 0.9707 (tt) cc_final: 0.9435 (pp) REVERT: B 128 MET cc_start: 0.9329 (tpp) cc_final: 0.8931 (tpp) REVERT: B 194 MET cc_start: 0.8984 (ppp) cc_final: 0.8701 (ppp) REVERT: B 277 CYS cc_start: 0.8164 (t) cc_final: 0.7599 (t) REVERT: B 301 ASN cc_start: 0.8804 (m-40) cc_final: 0.8440 (m-40) REVERT: B 302 TYR cc_start: 0.9326 (t80) cc_final: 0.9018 (t80) REVERT: B 307 PHE cc_start: 0.8795 (t80) cc_final: 0.8593 (t80) REVERT: B 323 ASN cc_start: 0.8838 (m-40) cc_final: 0.8169 (m-40) REVERT: B 385 PHE cc_start: 0.8736 (t80) cc_final: 0.8525 (m-80) REVERT: B 432 THR cc_start: 0.9306 (m) cc_final: 0.9076 (p) REVERT: B 472 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8956 (mt) REVERT: B 609 MET cc_start: 0.7621 (ptp) cc_final: 0.7252 (pmm) REVERT: B 614 LYS cc_start: 0.9531 (pmtt) cc_final: 0.9305 (tptp) REVERT: B 865 GLU cc_start: 0.9364 (mp0) cc_final: 0.9076 (mp0) REVERT: B 868 LYS cc_start: 0.9471 (mttt) cc_final: 0.9236 (mttt) REVERT: A 126 LEU cc_start: 0.9734 (tt) cc_final: 0.9443 (pp) REVERT: A 128 MET cc_start: 0.9410 (tpp) cc_final: 0.8982 (tpp) REVERT: A 173 LEU cc_start: 0.8987 (pp) cc_final: 0.8774 (pp) REVERT: A 194 MET cc_start: 0.8837 (ppp) cc_final: 0.8486 (ppp) REVERT: A 250 MET cc_start: 0.9139 (tpt) cc_final: 0.8934 (tpp) REVERT: A 277 CYS cc_start: 0.7868 (t) cc_final: 0.7333 (t) REVERT: A 301 ASN cc_start: 0.8730 (m-40) cc_final: 0.8333 (m-40) REVERT: A 302 TYR cc_start: 0.9336 (t80) cc_final: 0.9006 (t80) REVERT: A 323 ASN cc_start: 0.8910 (m-40) cc_final: 0.8260 (m-40) REVERT: A 432 THR cc_start: 0.9388 (m) cc_final: 0.9105 (p) REVERT: A 466 MET cc_start: 0.8711 (tpt) cc_final: 0.8471 (tpt) REVERT: A 472 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.8952 (tt) REVERT: A 865 GLU cc_start: 0.9546 (mp0) cc_final: 0.9319 (mp0) REVERT: A 868 LYS cc_start: 0.9536 (mttt) cc_final: 0.9322 (mttt) outliers start: 22 outliers final: 1 residues processed: 234 average time/residue: 0.2160 time to fit residues: 69.7997 Evaluate side-chains 135 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 132 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 472 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 68 optimal weight: 0.0570 chunk 107 optimal weight: 30.0000 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 451 HIS B 658 GLN A 451 HIS A 658 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9504 Z= 0.219 Angle : 0.907 12.802 12914 Z= 0.440 Chirality : 0.046 0.181 1526 Planarity : 0.006 0.050 1580 Dihedral : 7.051 51.009 1268 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.38 % Allowed : 16.30 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.69 (0.24), residues: 1182 helix: -0.27 (0.17), residues: 776 sheet: -0.20 (0.97), residues: 20 loop : -2.90 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 469 HIS 0.009 0.001 HIS B 838 PHE 0.040 0.002 PHE A 547 TYR 0.010 0.001 TYR B 137 ARG 0.005 0.001 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 172 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 128 MET cc_start: 0.9208 (tpp) cc_final: 0.8891 (tpp) REVERT: B 194 MET cc_start: 0.8857 (ppp) cc_final: 0.8552 (ppp) REVERT: B 302 TYR cc_start: 0.9406 (t80) cc_final: 0.9043 (t80) REVERT: B 504 MET cc_start: 0.9111 (tmm) cc_final: 0.8843 (tmm) REVERT: B 609 MET cc_start: 0.7812 (ptp) cc_final: 0.7432 (pmm) REVERT: B 826 PHE cc_start: 0.6720 (p90) cc_final: 0.6331 (p90) REVERT: A 128 MET cc_start: 0.9296 (tpp) cc_final: 0.8892 (tpp) REVERT: A 194 MET cc_start: 0.8675 (ppp) cc_final: 0.8327 (ppp) REVERT: A 250 MET cc_start: 0.9143 (tpt) cc_final: 0.8928 (tpp) REVERT: A 302 TYR cc_start: 0.9404 (t80) cc_final: 0.9072 (t80) REVERT: A 466 MET cc_start: 0.8761 (tpt) cc_final: 0.8278 (tpp) REVERT: A 470 MET cc_start: 0.8438 (mmm) cc_final: 0.7564 (mmm) REVERT: A 472 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.8999 (tt) REVERT: A 504 MET cc_start: 0.9035 (tmm) cc_final: 0.8649 (ppp) outliers start: 34 outliers final: 10 residues processed: 192 average time/residue: 0.1691 time to fit residues: 47.9551 Evaluate side-chains 144 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 133 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 614 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 89 optimal weight: 0.0060 chunk 72 optimal weight: 0.7980 chunk 29 optimal weight: 0.0670 chunk 107 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 36 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 overall best weight: 0.5334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9504 Z= 0.199 Angle : 0.886 13.710 12914 Z= 0.415 Chirality : 0.046 0.206 1526 Planarity : 0.005 0.049 1580 Dihedral : 6.013 43.815 1264 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 3.88 % Allowed : 17.50 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: -0.68 (0.25), residues: 1182 helix: 0.65 (0.19), residues: 756 sheet: -0.02 (0.99), residues: 20 loop : -2.66 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 469 HIS 0.006 0.001 HIS B 838 PHE 0.038 0.002 PHE A 547 TYR 0.011 0.001 TYR A 620 ARG 0.003 0.000 ARG B 669 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 159 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 128 MET cc_start: 0.9113 (tpp) cc_final: 0.8803 (tpp) REVERT: B 194 MET cc_start: 0.8905 (ppp) cc_final: 0.8568 (ppp) REVERT: B 246 LEU cc_start: 0.9796 (tp) cc_final: 0.9574 (tp) REVERT: B 302 TYR cc_start: 0.9456 (t80) cc_final: 0.8967 (t80) REVERT: B 502 MET cc_start: 0.9129 (tpp) cc_final: 0.8924 (tpp) REVERT: B 504 MET cc_start: 0.8934 (tmm) cc_final: 0.8662 (ppp) REVERT: B 548 GLU cc_start: 0.8787 (tt0) cc_final: 0.8545 (tt0) REVERT: B 609 MET cc_start: 0.8010 (ptp) cc_final: 0.7473 (pmm) REVERT: B 826 PHE cc_start: 0.6573 (p90) cc_final: 0.6311 (p90) REVERT: A 128 MET cc_start: 0.9239 (tpp) cc_final: 0.8930 (tpp) REVERT: A 194 MET cc_start: 0.8705 (ppp) cc_final: 0.8349 (ppp) REVERT: A 302 TYR cc_start: 0.9454 (t80) cc_final: 0.8996 (t80) REVERT: A 466 MET cc_start: 0.8702 (tpt) cc_final: 0.8398 (tpp) REVERT: A 470 MET cc_start: 0.8395 (mmm) cc_final: 0.7511 (mmm) REVERT: A 548 GLU cc_start: 0.8917 (tt0) cc_final: 0.8653 (tt0) REVERT: A 826 PHE cc_start: 0.6665 (p90) cc_final: 0.6148 (p90) outliers start: 39 outliers final: 18 residues processed: 184 average time/residue: 0.1532 time to fit residues: 42.8813 Evaluate side-chains 154 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 614 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 11 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 chunk 114 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 323 ASN B 436 HIS B 567 ASN A 436 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9504 Z= 0.309 Angle : 0.883 14.310 12914 Z= 0.431 Chirality : 0.048 0.218 1526 Planarity : 0.005 0.043 1580 Dihedral : 5.795 43.128 1264 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 4.87 % Allowed : 17.89 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: -0.34 (0.25), residues: 1182 helix: 0.92 (0.18), residues: 758 sheet: -0.00 (0.99), residues: 20 loop : -2.55 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 469 HIS 0.005 0.001 HIS A 369 PHE 0.029 0.002 PHE A 547 TYR 0.010 0.001 TYR B 137 ARG 0.003 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 137 time to evaluate : 0.975 Fit side-chains REVERT: B 135 MET cc_start: 0.9541 (ptp) cc_final: 0.9257 (ptp) REVERT: B 194 MET cc_start: 0.8892 (ppp) cc_final: 0.8444 (ppp) REVERT: B 246 LEU cc_start: 0.9800 (tp) cc_final: 0.9579 (tp) REVERT: B 302 TYR cc_start: 0.9520 (t80) cc_final: 0.8964 (t80) REVERT: B 391 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8573 (tp) REVERT: B 609 MET cc_start: 0.8085 (ptp) cc_final: 0.7541 (pmm) REVERT: A 128 MET cc_start: 0.9334 (tpp) cc_final: 0.9134 (tpp) REVERT: A 135 MET cc_start: 0.9540 (ptp) cc_final: 0.9245 (ptp) REVERT: A 194 MET cc_start: 0.8722 (ppp) cc_final: 0.8346 (ppp) REVERT: A 302 TYR cc_start: 0.9511 (t80) cc_final: 0.9014 (t80) REVERT: A 466 MET cc_start: 0.8739 (tpt) cc_final: 0.8282 (tpp) REVERT: A 470 MET cc_start: 0.8481 (mmm) cc_final: 0.7563 (mmm) REVERT: A 854 MET cc_start: 0.8631 (tmm) cc_final: 0.8281 (tmm) outliers start: 49 outliers final: 25 residues processed: 171 average time/residue: 0.1508 time to fit residues: 39.8992 Evaluate side-chains 147 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 121 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 614 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 0.0970 chunk 64 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 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 323 ASN B 567 ASN A 323 ASN A 838 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9504 Z= 0.213 Angle : 0.870 13.976 12914 Z= 0.404 Chirality : 0.046 0.216 1526 Planarity : 0.005 0.055 1580 Dihedral : 5.576 43.411 1264 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.98 % Allowed : 20.97 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.05 (0.25), residues: 1182 helix: 1.28 (0.19), residues: 760 sheet: -0.15 (0.98), residues: 20 loop : -2.50 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 469 HIS 0.006 0.001 HIS B 838 PHE 0.032 0.002 PHE A 547 TYR 0.011 0.001 TYR A 137 ARG 0.002 0.000 ARG B 334 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 140 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: B 128 MET cc_start: 0.9054 (tpp) cc_final: 0.8745 (tpp) REVERT: B 160 GLN cc_start: 0.9182 (mt0) cc_final: 0.8798 (mp10) REVERT: B 194 MET cc_start: 0.8854 (ppp) cc_final: 0.8543 (ppp) REVERT: B 246 LEU cc_start: 0.9772 (tp) cc_final: 0.9564 (tp) REVERT: B 302 TYR cc_start: 0.9476 (t80) cc_final: 0.8978 (t80) REVERT: B 339 MET cc_start: 0.8951 (ptt) cc_final: 0.8637 (ptp) REVERT: B 391 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8675 (tp) REVERT: B 466 MET cc_start: 0.8855 (mmm) cc_final: 0.8649 (mmm) REVERT: B 470 MET cc_start: 0.8390 (mmm) cc_final: 0.8168 (mmm) REVERT: B 609 MET cc_start: 0.8192 (ptp) cc_final: 0.7573 (pmm) REVERT: B 826 PHE cc_start: 0.6707 (p90) cc_final: 0.6391 (p90) REVERT: A 194 MET cc_start: 0.8723 (ppp) cc_final: 0.8432 (ppp) REVERT: A 302 TYR cc_start: 0.9476 (t80) cc_final: 0.8969 (t80) REVERT: A 466 MET cc_start: 0.8698 (tpt) cc_final: 0.8372 (tpp) REVERT: A 470 MET cc_start: 0.8391 (mmm) cc_final: 0.7644 (mmm) REVERT: A 838 HIS cc_start: 0.8325 (OUTLIER) cc_final: 0.8019 (t-90) outliers start: 40 outliers final: 19 residues processed: 167 average time/residue: 0.1473 time to fit residues: 38.4525 Evaluate side-chains 150 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 129 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 838 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 114 optimal weight: 0.0070 chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 overall best weight: 1.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 323 ASN B 567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9504 Z= 0.225 Angle : 0.900 16.591 12914 Z= 0.417 Chirality : 0.047 0.218 1526 Planarity : 0.005 0.071 1580 Dihedral : 5.416 44.734 1264 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 3.98 % Allowed : 20.78 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.23 (0.25), residues: 1182 helix: 1.42 (0.19), residues: 752 sheet: -0.31 (0.98), residues: 20 loop : -2.35 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 469 HIS 0.015 0.001 HIS B 369 PHE 0.029 0.001 PHE A 547 TYR 0.009 0.001 TYR A 524 ARG 0.001 0.000 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 129 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: B 135 MET cc_start: 0.9532 (ptp) cc_final: 0.9217 (ptp) REVERT: B 160 GLN cc_start: 0.9213 (mt0) cc_final: 0.8804 (mp10) REVERT: B 194 MET cc_start: 0.8882 (ppp) cc_final: 0.8577 (ppp) REVERT: B 246 LEU cc_start: 0.9777 (tp) cc_final: 0.9568 (tp) REVERT: B 250 MET cc_start: 0.9134 (tpp) cc_final: 0.8856 (tpt) REVERT: B 302 TYR cc_start: 0.9473 (t80) cc_final: 0.8961 (t80) REVERT: B 466 MET cc_start: 0.8805 (mmm) cc_final: 0.8362 (mmm) REVERT: B 470 MET cc_start: 0.8533 (mmm) cc_final: 0.8321 (mmm) REVERT: B 609 MET cc_start: 0.8195 (ptp) cc_final: 0.7563 (pmm) REVERT: A 135 MET cc_start: 0.9542 (ptp) cc_final: 0.9215 (ptp) REVERT: A 153 MET cc_start: 0.8887 (ppp) cc_final: 0.8632 (ppp) REVERT: A 194 MET cc_start: 0.8765 (ppp) cc_final: 0.8452 (ppp) REVERT: A 302 TYR cc_start: 0.9475 (t80) cc_final: 0.9008 (t80) REVERT: A 466 MET cc_start: 0.8688 (tpt) cc_final: 0.8458 (tpp) REVERT: A 470 MET cc_start: 0.8673 (mmm) cc_final: 0.8187 (mmm) REVERT: A 826 PHE cc_start: 0.6592 (p90) cc_final: 0.6216 (p90) outliers start: 40 outliers final: 30 residues processed: 155 average time/residue: 0.1428 time to fit residues: 34.3274 Evaluate side-chains 151 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 121 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 838 HIS Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 590 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 323 ASN B 567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9504 Z= 0.237 Angle : 0.913 13.910 12914 Z= 0.424 Chirality : 0.047 0.221 1526 Planarity : 0.005 0.061 1580 Dihedral : 5.369 46.184 1264 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.87 % Allowed : 21.07 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.34 (0.25), residues: 1182 helix: 1.50 (0.19), residues: 756 sheet: -0.32 (1.00), residues: 20 loop : -2.34 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 469 HIS 0.015 0.001 HIS B 369 PHE 0.032 0.002 PHE A 547 TYR 0.010 0.001 TYR A 137 ARG 0.002 0.000 ARG B 334 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 130 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.8847 (ppp) cc_final: 0.8610 (ppp) REVERT: B 178 PHE cc_start: 0.9272 (OUTLIER) cc_final: 0.8933 (m-80) REVERT: B 194 MET cc_start: 0.8858 (ppp) cc_final: 0.8562 (ppp) REVERT: B 246 LEU cc_start: 0.9772 (tp) cc_final: 0.9566 (tp) REVERT: B 302 TYR cc_start: 0.9485 (t80) cc_final: 0.9005 (t80) REVERT: B 325 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7774 (p0) REVERT: B 466 MET cc_start: 0.8762 (mmm) cc_final: 0.8398 (mmm) REVERT: B 609 MET cc_start: 0.8197 (ptp) cc_final: 0.7596 (pmm) REVERT: B 826 PHE cc_start: 0.6690 (p90) cc_final: 0.6390 (p90) REVERT: A 178 PHE cc_start: 0.9224 (OUTLIER) cc_final: 0.8767 (m-80) REVERT: A 194 MET cc_start: 0.8733 (ppp) cc_final: 0.8413 (ppp) REVERT: A 273 VAL cc_start: 0.9175 (t) cc_final: 0.8912 (m) REVERT: A 302 TYR cc_start: 0.9482 (t80) cc_final: 0.9004 (t80) REVERT: A 470 MET cc_start: 0.8744 (mmm) cc_final: 0.8451 (mmm) outliers start: 49 outliers final: 32 residues processed: 160 average time/residue: 0.1596 time to fit residues: 38.9914 Evaluate side-chains 156 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 121 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 301 ASN Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 615 PHE Chi-restraints excluded: chain B residue 838 HIS Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 568 MET Chi-restraints excluded: chain A residue 581 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.0980 chunk 45 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 323 ASN B 567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9504 Z= 0.210 Angle : 0.937 14.452 12914 Z= 0.427 Chirality : 0.047 0.222 1526 Planarity : 0.005 0.058 1580 Dihedral : 5.251 44.718 1264 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.68 % Allowed : 22.27 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.43 (0.25), residues: 1182 helix: 1.55 (0.19), residues: 756 sheet: -0.26 (1.02), residues: 20 loop : -2.24 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 469 HIS 0.010 0.001 HIS B 369 PHE 0.032 0.002 PHE A 547 TYR 0.010 0.001 TYR B 137 ARG 0.002 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 137 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: B 153 MET cc_start: 0.8835 (ppp) cc_final: 0.8624 (ppp) REVERT: B 178 PHE cc_start: 0.9259 (OUTLIER) cc_final: 0.9011 (m-80) REVERT: B 194 MET cc_start: 0.8868 (ppp) cc_final: 0.8627 (ppp) REVERT: B 302 TYR cc_start: 0.9465 (t80) cc_final: 0.8954 (t80) REVERT: B 325 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7722 (p0) REVERT: B 466 MET cc_start: 0.8845 (mmm) cc_final: 0.8284 (mmm) REVERT: B 504 MET cc_start: 0.9159 (tmm) cc_final: 0.8942 (ppp) REVERT: B 609 MET cc_start: 0.8278 (ptp) cc_final: 0.7627 (pmm) REVERT: B 826 PHE cc_start: 0.6543 (p90) cc_final: 0.6205 (p90) REVERT: A 178 PHE cc_start: 0.9209 (OUTLIER) cc_final: 0.8728 (m-80) REVERT: A 194 MET cc_start: 0.8726 (ppp) cc_final: 0.8404 (ppp) REVERT: A 302 TYR cc_start: 0.9450 (t80) cc_final: 0.8985 (t80) REVERT: A 826 PHE cc_start: 0.6787 (p90) cc_final: 0.6424 (p90) outliers start: 37 outliers final: 26 residues processed: 162 average time/residue: 0.1468 time to fit residues: 37.2547 Evaluate side-chains 157 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 128 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 838 HIS Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 568 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 chunk 63 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 0.3980 chunk 95 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 567 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9504 Z= 0.212 Angle : 0.966 14.322 12914 Z= 0.434 Chirality : 0.048 0.263 1526 Planarity : 0.004 0.057 1580 Dihedral : 5.207 44.193 1264 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.08 % Allowed : 23.26 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.41 (0.26), residues: 1182 helix: 1.53 (0.19), residues: 756 sheet: -0.24 (1.04), residues: 20 loop : -2.22 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 469 HIS 0.010 0.001 HIS B 369 PHE 0.030 0.001 PHE B 547 TYR 0.009 0.001 TYR B 524 ARG 0.002 0.000 ARG B 334 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 142 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 194 MET cc_start: 0.8863 (ppp) cc_final: 0.8585 (ppp) REVERT: B 302 TYR cc_start: 0.9459 (t80) cc_final: 0.8969 (t80) REVERT: B 325 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7643 (p0) REVERT: B 332 LEU cc_start: 0.9029 (mt) cc_final: 0.8789 (tp) REVERT: B 609 MET cc_start: 0.8280 (ptp) cc_final: 0.7604 (pmm) REVERT: B 826 PHE cc_start: 0.6409 (p90) cc_final: 0.6060 (p90) REVERT: A 178 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8848 (m-80) REVERT: A 194 MET cc_start: 0.8745 (ppp) cc_final: 0.8425 (ppp) REVERT: A 302 TYR cc_start: 0.9458 (t80) cc_final: 0.9002 (t80) outliers start: 31 outliers final: 24 residues processed: 159 average time/residue: 0.1496 time to fit residues: 36.9605 Evaluate side-chains 159 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 133 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 301 ASN Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain B residue 615 PHE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 557 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 117 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 567 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9504 Z= 0.227 Angle : 0.976 14.367 12914 Z= 0.440 Chirality : 0.048 0.288 1526 Planarity : 0.004 0.055 1580 Dihedral : 5.209 44.193 1264 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.28 % Allowed : 23.26 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.39 (0.25), residues: 1182 helix: 1.49 (0.19), residues: 756 sheet: -0.19 (1.04), residues: 20 loop : -2.20 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 469 HIS 0.008 0.001 HIS B 369 PHE 0.029 0.001 PHE A 547 TYR 0.009 0.001 TYR B 146 ARG 0.002 0.000 ARG B 334 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 137 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 194 MET cc_start: 0.8906 (ppp) cc_final: 0.8619 (ppp) REVERT: B 302 TYR cc_start: 0.9474 (t80) cc_final: 0.9037 (t80) REVERT: B 325 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7652 (p0) REVERT: B 609 MET cc_start: 0.8237 (ptp) cc_final: 0.7642 (pmm) REVERT: A 178 PHE cc_start: 0.9171 (OUTLIER) cc_final: 0.8886 (m-80) REVERT: A 194 MET cc_start: 0.8742 (ppp) cc_final: 0.8430 (ppp) REVERT: A 302 TYR cc_start: 0.9468 (t80) cc_final: 0.9059 (t80) REVERT: A 826 PHE cc_start: 0.6750 (p90) cc_final: 0.6406 (p90) outliers start: 33 outliers final: 29 residues processed: 156 average time/residue: 0.1597 time to fit residues: 38.9039 Evaluate side-chains 164 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 133 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 301 ASN Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 559 MET Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 615 PHE Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 838 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.1980 chunk 86 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 567 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.076334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.056382 restraints weight = 40700.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.058062 restraints weight = 23859.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.059049 restraints weight = 16382.332| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.5643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9504 Z= 0.215 Angle : 0.996 14.716 12914 Z= 0.445 Chirality : 0.048 0.282 1526 Planarity : 0.005 0.056 1580 Dihedral : 5.194 43.423 1264 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.88 % Allowed : 24.16 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.43 (0.25), residues: 1182 helix: 1.49 (0.19), residues: 754 sheet: -0.15 (1.05), residues: 20 loop : -2.10 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 469 HIS 0.008 0.001 HIS B 369 PHE 0.029 0.001 PHE A 547 TYR 0.009 0.001 TYR B 524 ARG 0.001 0.000 ARG A 654 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1796.33 seconds wall clock time: 33 minutes 20.55 seconds (2000.55 seconds total)