Starting phenix.real_space_refine on Tue Jul 29 16:11:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xbl_38222/07_2025/8xbl_38222.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xbl_38222/07_2025/8xbl_38222.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xbl_38222/07_2025/8xbl_38222.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xbl_38222/07_2025/8xbl_38222.map" model { file = "/net/cci-nas-00/data/ceres_data/8xbl_38222/07_2025/8xbl_38222.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xbl_38222/07_2025/8xbl_38222.cif" } resolution = 3.06 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 58 5.16 5 C 7285 2.51 5 N 2011 2.21 5 O 2155 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11509 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 5758 Classifications: {'peptide': 749} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 705} Chain: "B" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 5751 Classifications: {'peptide': 748} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 704} Time building chain proxies: 8.33, per 1000 atoms: 0.72 Number of scatterers: 11509 At special positions: 0 Unit cell: (99.825, 96.525, 152.625, 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 58 16.00 O 2155 8.00 N 2011 7.00 C 7285 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: 2.88 Conformation dependent library (CDL) restraints added in 1.6 seconds 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2754 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 14 sheets defined 38.8% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 26 through 37 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 85 through 92 Processing helix chain 'A' and resid 93 through 111 Processing helix chain 'A' and resid 130 through 140 removed outlier: 3.741A pdb=" N LEU A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 155 Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 159 through 169 Processing helix chain 'A' and resid 182 through 197 Processing helix chain 'A' and resid 256 through 262 Processing helix chain 'A' and resid 289 through 304 Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 323 through 336 removed outlier: 3.659A pdb=" N ILE A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 359 through 375 Processing helix chain 'A' and resid 407 through 411 removed outlier: 3.509A pdb=" N ARG A 410 " --> pdb=" O PRO A 407 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET A 411 " --> pdb=" O ALA A 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 407 through 411' Processing helix chain 'A' and resid 457 through 475 removed outlier: 4.162A pdb=" N THR A 469 " --> pdb=" O THR A 465 " (cutoff:3.500A) Proline residue: A 470 - end of helix Processing helix chain 'A' and resid 476 through 487 Processing helix chain 'A' and resid 544 through 558 removed outlier: 4.355A pdb=" N GLY A 558 " --> pdb=" O ALA A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 596 Processing helix chain 'A' and resid 609 through 618 Processing helix chain 'A' and resid 621 through 635 removed outlier: 3.609A pdb=" N VAL A 625 " --> pdb=" O ALA A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 678 removed outlier: 4.297A pdb=" N TRP A 671 " --> pdb=" O ASP A 667 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 672 " --> pdb=" O ARG A 668 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 713 Processing helix chain 'A' and resid 719 through 723 Processing helix chain 'B' and resid 26 through 36 Processing helix chain 'B' and resid 45 through 53 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 85 through 91 Processing helix chain 'B' and resid 95 through 110 Processing helix chain 'B' and resid 130 through 139 Processing helix chain 'B' and resid 144 through 155 Processing helix chain 'B' and resid 156 through 158 No H-bonds generated for 'chain 'B' and resid 156 through 158' Processing helix chain 'B' and resid 159 through 169 Processing helix chain 'B' and resid 182 through 197 Processing helix chain 'B' and resid 256 through 262 Processing helix chain 'B' and resid 289 through 304 Processing helix chain 'B' and resid 323 through 336 removed outlier: 3.559A pdb=" N ILE B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 354 Processing helix chain 'B' and resid 359 through 375 Processing helix chain 'B' and resid 457 through 467 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 476 through 487 Processing helix chain 'B' and resid 542 through 557 Processing helix chain 'B' and resid 578 through 597 Processing helix chain 'B' and resid 609 through 618 Processing helix chain 'B' and resid 621 through 635 Processing helix chain 'B' and resid 668 through 676 removed outlier: 3.520A pdb=" N SER B 672 " --> pdb=" O ARG B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 714 removed outlier: 4.202A pdb=" N LEU B 705 " --> pdb=" O ASP B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 723 Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 177 removed outlier: 8.357A pdb=" N TYR A 175 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL A 123 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU A 177 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL A 125 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 175 through 177 removed outlier: 8.357A pdb=" N TYR A 175 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL A 123 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU A 177 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL A 125 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 248 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL A 19 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL A 250 " --> pdb=" O MET A 17 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET A 17 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL A 252 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA A 268 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE A 430 " --> pdb=" O ARG A 271 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER A 273 " --> pdb=" O HIS A 428 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N HIS A 428 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL A 275 " --> pdb=" O ASN A 426 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASN A 426 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ARG A 414 " --> pdb=" O ILE A 311 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR A 313 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLY A 312 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N GLY A 347 " --> pdb=" O GLY A 312 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL A 314 " --> pdb=" O GLY A 347 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N CYS A 344 " --> pdb=" O TYR A 398 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.624A pdb=" N LYS A 68 " --> pdb=" O THR A 42 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 77 Processing sheet with id=AA5, first strand: chain 'A' and resid 376 through 377 Processing sheet with id=AA6, first strand: chain 'A' and resid 449 through 455 Processing sheet with id=AA7, first strand: chain 'A' and resid 652 through 654 removed outlier: 6.336A pdb=" N TRP A 520 " --> pdb=" O LEU A 602 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N SER A 604 " --> pdb=" O TRP A 520 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU A 522 " --> pdb=" O SER A 604 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 174 through 176 removed outlier: 8.415A pdb=" N TYR B 175 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL B 123 " --> pdb=" O TYR B 175 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA B 248 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL B 19 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL B 250 " --> pdb=" O MET B 17 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N MET B 17 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL B 252 " --> pdb=" O ILE B 15 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA B 268 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ILE B 270 " --> pdb=" O GLU B 432 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLU B 432 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY B 272 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ARG B 414 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR B 313 " --> pdb=" O ARG B 414 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.841A pdb=" N THR B 42 " --> pdb=" O LYS B 68 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 64 through 65 Processing sheet with id=AB2, first strand: chain 'B' and resid 76 through 77 Processing sheet with id=AB3, first strand: chain 'B' and resid 376 through 377 Processing sheet with id=AB4, first strand: chain 'B' and resid 449 through 455 Processing sheet with id=AB5, first strand: chain 'B' and resid 600 through 602 removed outlier: 7.278A pdb=" N TRP B 520 " --> pdb=" O THR B 601 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1356 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: 4.06 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2395 1.32 - 1.45: 2946 1.45 - 1.57: 6386 1.57 - 1.70: 0 1.70 - 1.82: 84 Bond restraints: 11811 Sorted by residual: bond pdb=" CA ILE B 561 " pdb=" C ILE B 561 " ideal model delta sigma weight residual 1.524 1.495 0.030 1.05e-02 9.07e+03 7.95e+00 bond pdb=" C PRO B 94 " pdb=" O PRO B 94 " ideal model delta sigma weight residual 1.235 1.199 0.036 1.30e-02 5.92e+03 7.69e+00 bond pdb=" CG LEU B 480 " pdb=" CD1 LEU B 480 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.54e+00 bond pdb=" CG1 ILE B 210 " pdb=" CD1 ILE B 210 " ideal model delta sigma weight residual 1.513 1.411 0.102 3.90e-02 6.57e+02 6.80e+00 bond pdb=" CB MET B 429 " pdb=" CG MET B 429 " ideal model delta sigma weight residual 1.520 1.442 0.078 3.00e-02 1.11e+03 6.68e+00 ... (remaining 11806 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 15402 2.42 - 4.84: 593 4.84 - 7.25: 91 7.25 - 9.67: 33 9.67 - 12.09: 3 Bond angle restraints: 16122 Sorted by residual: angle pdb=" N LYS B 95 " pdb=" CA LYS B 95 " pdb=" C LYS B 95 " ideal model delta sigma weight residual 114.04 105.46 8.58 1.24e+00 6.50e-01 4.79e+01 angle pdb=" N ASN A 595 " pdb=" CA ASN A 595 " pdb=" C ASN A 595 " ideal model delta sigma weight residual 111.14 104.67 6.47 1.08e+00 8.57e-01 3.58e+01 angle pdb=" C ILE B 561 " pdb=" N PRO B 562 " pdb=" CA PRO B 562 " ideal model delta sigma weight residual 120.38 115.35 5.03 1.03e+00 9.43e-01 2.39e+01 angle pdb=" N GLU A 631 " pdb=" CA GLU A 631 " pdb=" CB GLU A 631 " ideal model delta sigma weight residual 110.28 117.81 -7.53 1.55e+00 4.16e-01 2.36e+01 angle pdb=" C THR A 179 " pdb=" N SER A 180 " pdb=" CA SER A 180 " ideal model delta sigma weight residual 121.54 130.54 -9.00 1.91e+00 2.74e-01 2.22e+01 ... (remaining 16117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 6168 17.83 - 35.65: 642 35.65 - 53.48: 94 53.48 - 71.30: 26 71.30 - 89.13: 16 Dihedral angle restraints: 6946 sinusoidal: 2647 harmonic: 4299 Sorted by residual: dihedral pdb=" CA HIS A 541 " pdb=" C HIS A 541 " pdb=" N SER A 542 " pdb=" CA SER A 542 " ideal model delta harmonic sigma weight residual 180.00 -150.43 -29.57 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA ASP B 211 " pdb=" C ASP B 211 " pdb=" N LEU B 212 " pdb=" CA LEU B 212 " ideal model delta harmonic sigma weight residual 180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA MET A 224 " pdb=" C MET A 224 " pdb=" N ILE A 225 " pdb=" CA ILE A 225 " ideal model delta harmonic sigma weight residual 180.00 153.99 26.01 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 6943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1360 0.071 - 0.142: 347 0.142 - 0.214: 53 0.214 - 0.285: 16 0.285 - 0.356: 6 Chirality restraints: 1782 Sorted by residual: chirality pdb=" CB VAL B 362 " pdb=" CA VAL B 362 " pdb=" CG1 VAL B 362 " pdb=" CG2 VAL B 362 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CB VAL A 362 " pdb=" CA VAL A 362 " pdb=" CG1 VAL A 362 " pdb=" CG2 VAL A 362 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CB THR B 534 " pdb=" CA THR B 534 " pdb=" OG1 THR B 534 " pdb=" CG2 THR B 534 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.35 2.00e-01 2.50e+01 3.10e+00 ... (remaining 1779 not shown) Planarity restraints: 2117 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 630 " 0.025 2.00e-02 2.50e+03 2.09e-02 1.09e+01 pdb=" CG TRP A 630 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP A 630 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 630 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 630 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 630 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 630 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 630 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 630 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 630 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 357 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.26e+00 pdb=" C HIS B 357 " 0.053 2.00e-02 2.50e+03 pdb=" O HIS B 357 " -0.020 2.00e-02 2.50e+03 pdb=" N ALA B 358 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 611 " -0.050 5.00e-02 4.00e+02 7.44e-02 8.87e+00 pdb=" N PRO A 612 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 612 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 612 " -0.042 5.00e-02 4.00e+02 ... (remaining 2114 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2194 2.76 - 3.30: 10837 3.30 - 3.83: 20673 3.83 - 4.37: 25014 4.37 - 4.90: 41502 Nonbonded interactions: 100220 Sorted by model distance: nonbonded pdb=" OE2 GLU A 309 " pdb=" OG1 THR A 338 " model vdw 2.229 3.040 nonbonded pdb=" OG1 THR A 483 " pdb=" O ARG A 731 " model vdw 2.234 3.040 nonbonded pdb=" O PRO B 308 " pdb=" OH TYR B 343 " model vdw 2.257 3.040 nonbonded pdb=" O SER B 96 " pdb=" ND1 HIS B 100 " model vdw 2.263 3.120 nonbonded pdb=" O ARG B 582 " pdb=" OG1 THR B 586 " model vdw 2.274 3.040 ... (remaining 100215 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 749) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.790 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.360 Find NCS groups from input model: 0.440 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: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 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 : 0.011 0.102 11811 Z= 0.468 Angle : 1.111 12.091 16122 Z= 0.593 Chirality : 0.068 0.356 1782 Planarity : 0.008 0.074 2117 Dihedral : 15.273 89.127 4192 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.97 % Favored : 92.90 % Rotamer: Outliers : 0.58 % Allowed : 0.50 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -2.60 (0.19), residues: 1493 helix: -1.80 (0.18), residues: 539 sheet: -1.05 (0.36), residues: 212 loop : -1.80 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP A 630 HIS 0.016 0.002 HIS A 317 PHE 0.022 0.003 PHE B 197 TYR 0.024 0.003 TYR B 535 ARG 0.022 0.001 ARG A 693 Details of bonding type rmsd hydrogen bonds : bond 0.13991 ( 466) hydrogen bonds : angle 7.91058 ( 1356) covalent geometry : bond 0.01109 (11811) covalent geometry : angle 1.11126 (16122) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 1.135 Fit side-chains REVERT: B 582 ARG cc_start: 0.6491 (mtm110) cc_final: 0.5857 (mtm110) outliers start: 7 outliers final: 1 residues processed: 121 average time/residue: 0.2324 time to fit residues: 41.0468 Evaluate side-chains 94 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 0.0370 chunk 116 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 134 optimal weight: 20.0000 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 HIS A 56 GLN A 460 GLN A 658 ASN B 56 GLN ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 HIS B 501 ASN B 560 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.147036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.104224 restraints weight = 15112.899| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.39 r_work: 0.2998 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11811 Z= 0.139 Angle : 0.622 7.221 16122 Z= 0.320 Chirality : 0.044 0.222 1782 Planarity : 0.005 0.061 2117 Dihedral : 5.953 58.773 1619 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.29 % Favored : 95.65 % Rotamer: Outliers : 0.83 % Allowed : 5.41 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -1.67 (0.20), residues: 1493 helix: -0.43 (0.21), residues: 543 sheet: -1.12 (0.37), residues: 205 loop : -1.58 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 133 HIS 0.008 0.001 HIS A 567 PHE 0.010 0.001 PHE B 197 TYR 0.016 0.001 TYR B 112 ARG 0.004 0.000 ARG B 115 Details of bonding type rmsd hydrogen bonds : bond 0.04239 ( 466) hydrogen bonds : angle 5.77955 ( 1356) covalent geometry : bond 0.00299 (11811) covalent geometry : angle 0.62153 (16122) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 1.154 Fit side-chains revert: symmetry clash REVERT: A 225 ILE cc_start: 0.7727 (tp) cc_final: 0.7429 (tp) REVERT: A 703 ASP cc_start: 0.8394 (t0) cc_final: 0.8043 (t0) outliers start: 10 outliers final: 7 residues processed: 114 average time/residue: 0.2303 time to fit residues: 38.6757 Evaluate side-chains 97 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 658 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 88 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 113 optimal weight: 0.3980 chunk 137 optimal weight: 0.0270 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.0844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.144045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.097343 restraints weight = 15362.651| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.35 r_work: 0.2952 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11811 Z= 0.236 Angle : 0.656 7.919 16122 Z= 0.333 Chirality : 0.046 0.183 1782 Planarity : 0.005 0.057 2117 Dihedral : 5.794 58.992 1619 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.76 % Favored : 94.17 % Rotamer: Outliers : 1.42 % Allowed : 8.66 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -1.30 (0.21), residues: 1493 helix: 0.07 (0.21), residues: 540 sheet: -1.20 (0.37), residues: 205 loop : -1.44 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 133 HIS 0.007 0.001 HIS A 627 PHE 0.014 0.002 PHE B 21 TYR 0.020 0.002 TYR B 112 ARG 0.005 0.000 ARG B 115 Details of bonding type rmsd hydrogen bonds : bond 0.04213 ( 466) hydrogen bonds : angle 5.45725 ( 1356) covalent geometry : bond 0.00539 (11811) covalent geometry : angle 0.65611 (16122) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 1.164 Fit side-chains REVERT: A 225 ILE cc_start: 0.7766 (tp) cc_final: 0.7508 (tp) REVERT: A 630 TRP cc_start: 0.7348 (t60) cc_final: 0.6982 (t60) REVERT: A 703 ASP cc_start: 0.8463 (t0) cc_final: 0.8141 (t0) outliers start: 17 outliers final: 13 residues processed: 108 average time/residue: 0.2335 time to fit residues: 37.1922 Evaluate side-chains 101 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 658 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 62 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 138 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 ASN ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.145320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.102336 restraints weight = 15267.058| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.39 r_work: 0.2956 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11811 Z= 0.174 Angle : 0.608 7.774 16122 Z= 0.307 Chirality : 0.044 0.175 1782 Planarity : 0.004 0.054 2117 Dihedral : 5.546 59.999 1619 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.08 % Allowed : 10.57 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -1.02 (0.21), residues: 1493 helix: 0.45 (0.22), residues: 540 sheet: -1.17 (0.37), residues: 205 loop : -1.36 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 133 HIS 0.007 0.001 HIS A 627 PHE 0.010 0.001 PHE A 450 TYR 0.015 0.001 TYR B 112 ARG 0.003 0.000 ARG B 254 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 466) hydrogen bonds : angle 5.19800 ( 1356) covalent geometry : bond 0.00395 (11811) covalent geometry : angle 0.60776 (16122) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 1.165 Fit side-chains REVERT: A 225 ILE cc_start: 0.7811 (tp) cc_final: 0.7590 (tp) REVERT: A 630 TRP cc_start: 0.7478 (t60) cc_final: 0.7004 (t60) REVERT: A 703 ASP cc_start: 0.8459 (t0) cc_final: 0.8136 (t0) outliers start: 25 outliers final: 20 residues processed: 120 average time/residue: 0.2207 time to fit residues: 39.4667 Evaluate side-chains 110 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 686 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 4 optimal weight: 0.5980 chunk 115 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 145 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 3 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: A 634 GLN ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.146961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.104634 restraints weight = 15247.912| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.27 r_work: 0.2999 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11811 Z= 0.130 Angle : 0.579 7.670 16122 Z= 0.292 Chirality : 0.043 0.219 1782 Planarity : 0.004 0.051 2117 Dihedral : 5.311 59.806 1619 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.16 % Allowed : 11.57 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.84 (0.21), residues: 1493 helix: 0.73 (0.22), residues: 542 sheet: -1.17 (0.36), residues: 212 loop : -1.34 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 133 HIS 0.007 0.001 HIS A 627 PHE 0.007 0.001 PHE A 21 TYR 0.012 0.001 TYR B 104 ARG 0.002 0.000 ARG B 528 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 466) hydrogen bonds : angle 4.99760 ( 1356) covalent geometry : bond 0.00291 (11811) covalent geometry : angle 0.57882 (16122) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 1.159 Fit side-chains REVERT: A 594 MET cc_start: 0.8541 (mtp) cc_final: 0.8047 (mpp) REVERT: A 630 TRP cc_start: 0.7415 (t60) cc_final: 0.7190 (t60) REVERT: A 703 ASP cc_start: 0.8373 (t0) cc_final: 0.8049 (t0) REVERT: B 632 MET cc_start: 0.6784 (ttt) cc_final: 0.6461 (ttm) outliers start: 26 outliers final: 22 residues processed: 127 average time/residue: 0.2073 time to fit residues: 39.9593 Evaluate side-chains 117 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 634 GLN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 658 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 90 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 45 optimal weight: 0.0020 chunk 133 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 585 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.143375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.100854 restraints weight = 15324.908| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.36 r_work: 0.2937 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 11811 Z= 0.244 Angle : 0.650 8.352 16122 Z= 0.327 Chirality : 0.046 0.185 1782 Planarity : 0.005 0.050 2117 Dihedral : 5.449 59.938 1619 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.41 % Allowed : 12.32 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.88 (0.21), residues: 1493 helix: 0.63 (0.22), residues: 541 sheet: -1.06 (0.36), residues: 213 loop : -1.35 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 133 HIS 0.021 0.001 HIS A 627 PHE 0.012 0.002 PHE A 21 TYR 0.018 0.002 TYR B 112 ARG 0.003 0.000 ARG B 265 Details of bonding type rmsd hydrogen bonds : bond 0.03918 ( 466) hydrogen bonds : angle 5.13498 ( 1356) covalent geometry : bond 0.00565 (11811) covalent geometry : angle 0.64955 (16122) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 1.275 Fit side-chains REVERT: B 632 MET cc_start: 0.6765 (ttt) cc_final: 0.6408 (ttm) REVERT: B 660 ILE cc_start: 0.6119 (OUTLIER) cc_final: 0.5847 (tp) outliers start: 29 outliers final: 26 residues processed: 119 average time/residue: 0.2208 time to fit residues: 39.9949 Evaluate side-chains 117 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 702 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 30 optimal weight: 6.9990 chunk 126 optimal weight: 20.0000 chunk 33 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.145018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.102967 restraints weight = 15402.355| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.34 r_work: 0.2965 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11811 Z= 0.170 Angle : 0.614 9.186 16122 Z= 0.308 Chirality : 0.044 0.175 1782 Planarity : 0.004 0.050 2117 Dihedral : 5.343 59.395 1619 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.75 % Allowed : 12.82 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.85 (0.21), residues: 1493 helix: 0.71 (0.22), residues: 548 sheet: -1.05 (0.36), residues: 213 loop : -1.39 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 133 HIS 0.022 0.001 HIS A 627 PHE 0.009 0.001 PHE A 21 TYR 0.014 0.001 TYR B 112 ARG 0.004 0.000 ARG B 582 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 466) hydrogen bonds : angle 5.06911 ( 1356) covalent geometry : bond 0.00388 (11811) covalent geometry : angle 0.61449 (16122) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 98 time to evaluate : 1.202 Fit side-chains revert: symmetry clash REVERT: A 594 MET cc_start: 0.8561 (mtp) cc_final: 0.8018 (mpp) REVERT: A 703 ASP cc_start: 0.8470 (t0) cc_final: 0.8153 (t0) REVERT: B 468 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8495 (mt) REVERT: B 632 MET cc_start: 0.6644 (ttt) cc_final: 0.6292 (ttm) REVERT: B 660 ILE cc_start: 0.6087 (OUTLIER) cc_final: 0.5810 (tp) outliers start: 33 outliers final: 27 residues processed: 123 average time/residue: 0.2429 time to fit residues: 45.7920 Evaluate side-chains 123 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 634 GLN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 702 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 141 optimal weight: 20.0000 chunk 129 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 137 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 ASN ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.146192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.103942 restraints weight = 15198.580| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.28 r_work: 0.2997 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11811 Z= 0.136 Angle : 0.589 9.371 16122 Z= 0.294 Chirality : 0.043 0.176 1782 Planarity : 0.004 0.050 2117 Dihedral : 5.135 58.951 1619 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.75 % Allowed : 12.91 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.74 (0.21), residues: 1493 helix: 0.85 (0.22), residues: 554 sheet: -0.99 (0.36), residues: 208 loop : -1.40 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 133 HIS 0.021 0.001 HIS A 627 PHE 0.008 0.001 PHE A 21 TYR 0.020 0.001 TYR A 535 ARG 0.003 0.000 ARG B 582 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 466) hydrogen bonds : angle 4.92484 ( 1356) covalent geometry : bond 0.00307 (11811) covalent geometry : angle 0.58947 (16122) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 99 time to evaluate : 1.170 Fit side-chains REVERT: A 59 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7503 (mm) REVERT: A 630 TRP cc_start: 0.7475 (t60) cc_final: 0.7255 (t60) REVERT: A 703 ASP cc_start: 0.8411 (t0) cc_final: 0.8096 (t0) REVERT: B 468 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8389 (mt) REVERT: B 632 MET cc_start: 0.6568 (ttt) cc_final: 0.6205 (ttm) REVERT: B 660 ILE cc_start: 0.6067 (OUTLIER) cc_final: 0.5778 (tp) outliers start: 33 outliers final: 25 residues processed: 124 average time/residue: 0.2097 time to fit residues: 39.5278 Evaluate side-chains 124 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 702 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 75 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 135 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.146540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.101870 restraints weight = 15319.034| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.45 r_work: 0.3005 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11811 Z= 0.134 Angle : 0.590 9.066 16122 Z= 0.295 Chirality : 0.043 0.174 1782 Planarity : 0.004 0.050 2117 Dihedral : 5.066 58.898 1619 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.41 % Allowed : 13.32 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.72 (0.22), residues: 1493 helix: 0.86 (0.22), residues: 560 sheet: -0.95 (0.36), residues: 208 loop : -1.42 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 133 HIS 0.021 0.001 HIS A 627 PHE 0.008 0.001 PHE A 21 TYR 0.012 0.001 TYR B 104 ARG 0.004 0.000 ARG B 582 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 466) hydrogen bonds : angle 4.87754 ( 1356) covalent geometry : bond 0.00303 (11811) covalent geometry : angle 0.59020 (16122) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 1.153 Fit side-chains REVERT: A 630 TRP cc_start: 0.7448 (t60) cc_final: 0.6961 (t60) REVERT: A 703 ASP cc_start: 0.8408 (t0) cc_final: 0.8099 (t0) REVERT: B 468 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8286 (mt) REVERT: B 632 MET cc_start: 0.6580 (ttt) cc_final: 0.6364 (ttm) REVERT: B 660 ILE cc_start: 0.6101 (OUTLIER) cc_final: 0.5825 (tp) outliers start: 29 outliers final: 23 residues processed: 121 average time/residue: 0.2116 time to fit residues: 38.7784 Evaluate side-chains 122 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 702 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 67 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 137 optimal weight: 0.0050 chunk 123 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 overall best weight: 1.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.145854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.103447 restraints weight = 15234.584| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.34 r_work: 0.2970 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11811 Z= 0.170 Angle : 0.617 8.938 16122 Z= 0.307 Chirality : 0.044 0.173 1782 Planarity : 0.004 0.049 2117 Dihedral : 5.140 59.088 1619 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.50 % Allowed : 13.49 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.61 (0.22), residues: 1493 helix: 0.97 (0.22), residues: 548 sheet: -0.90 (0.37), residues: 206 loop : -1.32 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 133 HIS 0.020 0.001 HIS A 627 PHE 0.009 0.001 PHE A 21 TYR 0.024 0.001 TYR A 535 ARG 0.004 0.000 ARG B 582 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 466) hydrogen bonds : angle 4.93175 ( 1356) covalent geometry : bond 0.00388 (11811) covalent geometry : angle 0.61657 (16122) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2986 Ramachandran restraints generated. 1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 1.239 Fit side-chains REVERT: A 59 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7457 (mm) REVERT: A 385 MET cc_start: 0.8246 (mmm) cc_final: 0.8044 (mmp) REVERT: A 703 ASP cc_start: 0.8454 (t0) cc_final: 0.8131 (t0) REVERT: B 148 ARG cc_start: 0.5136 (tpt170) cc_final: 0.4438 (ttt90) REVERT: B 468 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8375 (mt) REVERT: B 632 MET cc_start: 0.6537 (ttt) cc_final: 0.6305 (ttm) REVERT: B 660 ILE cc_start: 0.6109 (OUTLIER) cc_final: 0.5819 (tp) outliers start: 30 outliers final: 25 residues processed: 122 average time/residue: 0.2240 time to fit residues: 41.4900 Evaluate side-chains 121 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 702 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 81 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 125 optimal weight: 0.0570 chunk 75 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 138 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.146790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.103987 restraints weight = 15221.716| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.40 r_work: 0.2992 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11811 Z= 0.129 Angle : 0.594 8.839 16122 Z= 0.297 Chirality : 0.043 0.175 1782 Planarity : 0.004 0.056 2117 Dihedral : 5.055 58.821 1619 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.41 % Allowed : 13.49 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.62 (0.22), residues: 1493 helix: 0.99 (0.22), residues: 554 sheet: -0.91 (0.37), residues: 202 loop : -1.36 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 630 HIS 0.020 0.001 HIS A 627 PHE 0.007 0.001 PHE A 21 TYR 0.012 0.001 TYR A 707 ARG 0.005 0.000 ARG B 582 Details of bonding type rmsd hydrogen bonds : bond 0.03430 ( 466) hydrogen bonds : angle 4.88094 ( 1356) covalent geometry : bond 0.00291 (11811) covalent geometry : angle 0.59419 (16122) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7567.36 seconds wall clock time: 131 minutes 24.38 seconds (7884.38 seconds total)