Starting phenix.real_space_refine on Tue Feb 11 22:06:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ggs_4399/02_2025/6ggs_4399.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ggs_4399/02_2025/6ggs_4399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ggs_4399/02_2025/6ggs_4399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ggs_4399/02_2025/6ggs_4399.map" model { file = "/net/cci-nas-00/data/ceres_data/6ggs_4399/02_2025/6ggs_4399.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ggs_4399/02_2025/6ggs_4399.cif" } resolution = 3.94 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 ------------------------------------------------------------------------------- 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= 0.040 sd= 0.257 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 40 5.16 5 C 4270 2.51 5 N 1200 2.21 5 O 1370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6880 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 688 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 2.23, per 1000 atoms: 0.32 Number of scatterers: 6880 At special positions: 0 Unit cell: (88.33, 89.54, 85.91, 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 40 16.00 O 1370 8.00 N 1200 7.00 C 4270 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: 1.70 Conformation dependent library (CDL) restraints added in 908.9 milliseconds 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1660 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 0 sheets defined 67.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'F' and resid 435 through 439 removed outlier: 4.119A pdb=" N TRP F 439 " --> pdb=" O ALA F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 443 through 449 removed outlier: 3.979A pdb=" N ASN F 449 " --> pdb=" O GLU F 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 461 removed outlier: 3.774A pdb=" N SER F 459 " --> pdb=" O CYS F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 465 Processing helix chain 'F' and resid 473 through 478 Processing helix chain 'F' and resid 482 through 487 Processing helix chain 'F' and resid 487 through 497 removed outlier: 3.577A pdb=" N THR F 493 " --> pdb=" O GLN F 489 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP F 495 " --> pdb=" O LEU F 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 506 removed outlier: 4.368A pdb=" N VAL F 504 " --> pdb=" O GLU F 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 439 removed outlier: 4.119A pdb=" N TRP A 439 " --> pdb=" O ALA A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 449 removed outlier: 3.979A pdb=" N ASN A 449 " --> pdb=" O GLU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 461 removed outlier: 3.773A pdb=" N SER A 459 " --> pdb=" O CYS A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 465 Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 487 through 497 removed outlier: 3.578A pdb=" N THR A 493 " --> pdb=" O GLN A 489 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 506 removed outlier: 4.369A pdb=" N VAL A 504 " --> pdb=" O GLU A 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 439 removed outlier: 4.120A pdb=" N TRP B 439 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 449 removed outlier: 3.979A pdb=" N ASN B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 461 removed outlier: 3.773A pdb=" N SER B 459 " --> pdb=" O CYS B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 465 Processing helix chain 'B' and resid 473 through 478 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 487 through 497 removed outlier: 3.578A pdb=" N THR B 493 " --> pdb=" O GLN B 489 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 506 removed outlier: 4.369A pdb=" N VAL B 504 " --> pdb=" O GLU B 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 439 removed outlier: 4.119A pdb=" N TRP C 439 " --> pdb=" O ALA C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 449 removed outlier: 3.979A pdb=" N ASN C 449 " --> pdb=" O GLU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 461 removed outlier: 3.774A pdb=" N SER C 459 " --> pdb=" O CYS C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 465 Processing helix chain 'C' and resid 473 through 478 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 487 through 497 removed outlier: 3.578A pdb=" N THR C 493 " --> pdb=" O GLN C 489 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 506 removed outlier: 4.368A pdb=" N VAL C 504 " --> pdb=" O GLU C 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 439 removed outlier: 4.119A pdb=" N TRP D 439 " --> pdb=" O ALA D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 449 removed outlier: 3.979A pdb=" N ASN D 449 " --> pdb=" O GLU D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 461 removed outlier: 3.774A pdb=" N SER D 459 " --> pdb=" O CYS D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 465 Processing helix chain 'D' and resid 473 through 478 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 487 through 497 removed outlier: 3.578A pdb=" N THR D 493 " --> pdb=" O GLN D 489 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 506 removed outlier: 4.369A pdb=" N VAL D 504 " --> pdb=" O GLU D 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 439 removed outlier: 4.119A pdb=" N TRP E 439 " --> pdb=" O ALA E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 449 removed outlier: 3.979A pdb=" N ASN E 449 " --> pdb=" O GLU E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 461 removed outlier: 3.773A pdb=" N SER E 459 " --> pdb=" O CYS E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 465 Processing helix chain 'E' and resid 473 through 478 Processing helix chain 'E' and resid 482 through 487 Processing helix chain 'E' and resid 487 through 497 removed outlier: 3.578A pdb=" N THR E 493 " --> pdb=" O GLN E 489 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP E 495 " --> pdb=" O LEU E 491 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 506 removed outlier: 4.369A pdb=" N VAL E 504 " --> pdb=" O GLU E 500 " (cutoff:3.500A) Processing helix chain 'G' and resid 435 through 439 removed outlier: 4.118A pdb=" N TRP G 439 " --> pdb=" O ALA G 436 " (cutoff:3.500A) Processing helix chain 'G' and resid 443 through 449 removed outlier: 3.979A pdb=" N ASN G 449 " --> pdb=" O GLU G 445 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 461 removed outlier: 3.774A pdb=" N SER G 459 " --> pdb=" O CYS G 455 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 465 Processing helix chain 'G' and resid 473 through 478 Processing helix chain 'G' and resid 482 through 487 Processing helix chain 'G' and resid 487 through 497 removed outlier: 3.577A pdb=" N THR G 493 " --> pdb=" O GLN G 489 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP G 495 " --> pdb=" O LEU G 491 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 506 removed outlier: 4.369A pdb=" N VAL G 504 " --> pdb=" O GLU G 500 " (cutoff:3.500A) Processing helix chain 'H' and resid 435 through 439 removed outlier: 4.119A pdb=" N TRP H 439 " --> pdb=" O ALA H 436 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 449 removed outlier: 3.979A pdb=" N ASN H 449 " --> pdb=" O GLU H 445 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 461 removed outlier: 3.774A pdb=" N SER H 459 " --> pdb=" O CYS H 455 " (cutoff:3.500A) Processing helix chain 'H' and resid 462 through 465 Processing helix chain 'H' and resid 473 through 478 Processing helix chain 'H' and resid 482 through 487 Processing helix chain 'H' and resid 487 through 497 removed outlier: 3.577A pdb=" N THR H 493 " --> pdb=" O GLN H 489 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP H 495 " --> pdb=" O LEU H 491 " (cutoff:3.500A) Processing helix chain 'H' and resid 498 through 506 removed outlier: 4.368A pdb=" N VAL H 504 " --> pdb=" O GLU H 500 " (cutoff:3.500A) Processing helix chain 'I' and resid 435 through 439 removed outlier: 4.119A pdb=" N TRP I 439 " --> pdb=" O ALA I 436 " (cutoff:3.500A) Processing helix chain 'I' and resid 443 through 449 removed outlier: 3.979A pdb=" N ASN I 449 " --> pdb=" O GLU I 445 " (cutoff:3.500A) Processing helix chain 'I' and resid 452 through 461 removed outlier: 3.774A pdb=" N SER I 459 " --> pdb=" O CYS I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 462 through 465 Processing helix chain 'I' and resid 473 through 478 Processing helix chain 'I' and resid 482 through 487 Processing helix chain 'I' and resid 487 through 497 removed outlier: 3.577A pdb=" N THR I 493 " --> pdb=" O GLN I 489 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP I 495 " --> pdb=" O LEU I 491 " (cutoff:3.500A) Processing helix chain 'I' and resid 498 through 506 removed outlier: 4.369A pdb=" N VAL I 504 " --> pdb=" O GLU I 500 " (cutoff:3.500A) Processing helix chain 'J' and resid 435 through 439 removed outlier: 4.119A pdb=" N TRP J 439 " --> pdb=" O ALA J 436 " (cutoff:3.500A) Processing helix chain 'J' and resid 443 through 449 removed outlier: 3.979A pdb=" N ASN J 449 " --> pdb=" O GLU J 445 " (cutoff:3.500A) Processing helix chain 'J' and resid 452 through 461 removed outlier: 3.774A pdb=" N SER J 459 " --> pdb=" O CYS J 455 " (cutoff:3.500A) Processing helix chain 'J' and resid 462 through 465 Processing helix chain 'J' and resid 473 through 478 Processing helix chain 'J' and resid 482 through 487 Processing helix chain 'J' and resid 487 through 497 removed outlier: 3.577A pdb=" N THR J 493 " --> pdb=" O GLN J 489 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP J 495 " --> pdb=" O LEU J 491 " (cutoff:3.500A) Processing helix chain 'J' and resid 498 through 506 removed outlier: 4.368A pdb=" N VAL J 504 " --> pdb=" O GLU J 500 " (cutoff:3.500A) 220 hydrogen bonds defined for protein. 600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.54 Time building geometry restraints manager: 1.97 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: 2295 1.34 - 1.45: 702 1.45 - 1.57: 3863 1.57 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 6930 Sorted by residual: bond pdb=" CG1 ILE H 496 " pdb=" CD1 ILE H 496 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.56e+00 bond pdb=" CG MET C 470 " pdb=" SD MET C 470 " ideal model delta sigma weight residual 1.803 1.772 0.031 2.50e-02 1.60e+03 1.55e+00 bond pdb=" CG MET J 470 " pdb=" SD MET J 470 " ideal model delta sigma weight residual 1.803 1.772 0.031 2.50e-02 1.60e+03 1.54e+00 bond pdb=" CG1 ILE D 496 " pdb=" CD1 ILE D 496 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.54e+00 bond pdb=" CG1 ILE G 496 " pdb=" CD1 ILE G 496 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.53e+00 ... (remaining 6925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 8751 2.16 - 4.33: 450 4.33 - 6.49: 59 6.49 - 8.65: 30 8.65 - 10.81: 10 Bond angle restraints: 9300 Sorted by residual: angle pdb=" CA LEU D 456 " pdb=" CB LEU D 456 " pdb=" CG LEU D 456 " ideal model delta sigma weight residual 116.30 127.11 -10.81 3.50e+00 8.16e-02 9.55e+00 angle pdb=" CA LEU J 456 " pdb=" CB LEU J 456 " pdb=" CG LEU J 456 " ideal model delta sigma weight residual 116.30 127.10 -10.80 3.50e+00 8.16e-02 9.53e+00 angle pdb=" CA LEU F 456 " pdb=" CB LEU F 456 " pdb=" CG LEU F 456 " ideal model delta sigma weight residual 116.30 127.10 -10.80 3.50e+00 8.16e-02 9.52e+00 angle pdb=" CA LEU B 456 " pdb=" CB LEU B 456 " pdb=" CG LEU B 456 " ideal model delta sigma weight residual 116.30 127.10 -10.80 3.50e+00 8.16e-02 9.52e+00 angle pdb=" CA LEU G 456 " pdb=" CB LEU G 456 " pdb=" CG LEU G 456 " ideal model delta sigma weight residual 116.30 127.10 -10.80 3.50e+00 8.16e-02 9.52e+00 ... (remaining 9295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.35: 3950 15.35 - 30.69: 360 30.69 - 46.04: 70 46.04 - 61.39: 20 61.39 - 76.74: 20 Dihedral angle restraints: 4420 sinusoidal: 1900 harmonic: 2520 Sorted by residual: dihedral pdb=" CA GLU C 472 " pdb=" C GLU C 472 " pdb=" N ASP C 473 " pdb=" CA ASP C 473 " ideal model delta harmonic sigma weight residual 180.00 160.17 19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLU F 472 " pdb=" C GLU F 472 " pdb=" N ASP F 473 " pdb=" CA ASP F 473 " ideal model delta harmonic sigma weight residual 180.00 160.20 19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLN H 489 " pdb=" C GLN H 489 " pdb=" N LEU H 490 " pdb=" CA LEU H 490 " ideal model delta harmonic sigma weight residual 180.00 160.20 19.80 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 4417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 513 0.040 - 0.081: 370 0.081 - 0.121: 157 0.121 - 0.162: 30 0.162 - 0.202: 30 Chirality restraints: 1100 Sorted by residual: chirality pdb=" CA GLU A 472 " pdb=" N GLU A 472 " pdb=" C GLU A 472 " pdb=" CB GLU A 472 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA GLU C 472 " pdb=" N GLU C 472 " pdb=" C GLU C 472 " pdb=" CB GLU C 472 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA GLU G 472 " pdb=" N GLU G 472 " pdb=" C GLU G 472 " pdb=" CB GLU G 472 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1097 not shown) Planarity restraints: 1190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL J 477 " 0.006 2.00e-02 2.50e+03 1.11e-02 1.22e+00 pdb=" C VAL J 477 " -0.019 2.00e-02 2.50e+03 pdb=" O VAL J 477 " 0.007 2.00e-02 2.50e+03 pdb=" N SER J 478 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 477 " -0.006 2.00e-02 2.50e+03 1.11e-02 1.22e+00 pdb=" C VAL H 477 " 0.019 2.00e-02 2.50e+03 pdb=" O VAL H 477 " -0.007 2.00e-02 2.50e+03 pdb=" N SER H 478 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 477 " 0.006 2.00e-02 2.50e+03 1.11e-02 1.22e+00 pdb=" C VAL B 477 " -0.019 2.00e-02 2.50e+03 pdb=" O VAL B 477 " 0.007 2.00e-02 2.50e+03 pdb=" N SER B 478 " 0.007 2.00e-02 2.50e+03 ... (remaining 1187 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 113 2.63 - 3.20: 6291 3.20 - 3.76: 11306 3.76 - 4.33: 16042 4.33 - 4.90: 23335 Nonbonded interactions: 57087 Sorted by model distance: nonbonded pdb=" OD1 ASP A 461 " pdb=" NE ARG D 444 " model vdw 2.060 3.120 nonbonded pdb=" OD1 ASP F 461 " pdb=" NE ARG I 444 " model vdw 2.060 3.120 nonbonded pdb=" OD1 ASP G 461 " pdb=" NE ARG J 444 " model vdw 2.061 3.120 nonbonded pdb=" OD1 ASP B 461 " pdb=" NE ARG E 444 " model vdw 2.061 3.120 nonbonded pdb=" OD1 ASP E 461 " pdb=" NE ARG H 444 " model vdw 2.061 3.120 ... (remaining 57082 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } 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: 0.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.370 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 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 : 0.006 0.049 6930 Z= 0.365 Angle : 1.154 10.815 9300 Z= 0.572 Chirality : 0.065 0.202 1100 Planarity : 0.004 0.012 1190 Dihedral : 14.099 76.735 2760 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.27 % Allowed : 7.59 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -6.91 (0.16), residues: 840 helix: -4.95 (0.07), residues: 530 sheet: None (None), residues: 0 loop : -3.50 (0.26), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP F 439 PHE 0.010 0.003 PHE J 501 TYR 0.005 0.002 TYR H 474 ARG 0.010 0.003 ARG I 488 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 399 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 439 TRP cc_start: 0.7854 (t60) cc_final: 0.7337 (t60) REVERT: F 443 LYS cc_start: 0.8792 (mmtt) cc_final: 0.8441 (mtpp) REVERT: F 453 GLU cc_start: 0.8492 (pp20) cc_final: 0.8076 (pp20) REVERT: F 457 ASN cc_start: 0.9153 (m110) cc_final: 0.8674 (m-40) REVERT: F 458 GLN cc_start: 0.8384 (pt0) cc_final: 0.8105 (pt0) REVERT: F 515 MET cc_start: 0.7086 (pp-130) cc_final: 0.6851 (pp-130) REVERT: A 439 TRP cc_start: 0.7645 (t60) cc_final: 0.6837 (t60) REVERT: A 453 GLU cc_start: 0.8477 (pp20) cc_final: 0.8013 (pp20) REVERT: A 457 ASN cc_start: 0.9084 (m110) cc_final: 0.8771 (m-40) REVERT: A 458 GLN cc_start: 0.8530 (pt0) cc_final: 0.8034 (pt0) REVERT: A 500 GLU cc_start: 0.6342 (mp0) cc_final: 0.6043 (mp0) REVERT: A 515 MET cc_start: 0.7258 (pp-130) cc_final: 0.6731 (pp-130) REVERT: B 443 LYS cc_start: 0.9008 (mmtt) cc_final: 0.8583 (mtpp) REVERT: B 447 ILE cc_start: 0.8607 (tt) cc_final: 0.8391 (tt) REVERT: B 453 GLU cc_start: 0.8600 (pp20) cc_final: 0.8090 (pp20) REVERT: B 457 ASN cc_start: 0.9177 (m110) cc_final: 0.8732 (m110) REVERT: B 458 GLN cc_start: 0.8635 (pt0) cc_final: 0.8227 (pt0) REVERT: B 482 THR cc_start: 0.8265 (t) cc_final: 0.7988 (t) REVERT: B 515 MET cc_start: 0.7310 (pp-130) cc_final: 0.6797 (pp-130) REVERT: C 439 TRP cc_start: 0.8076 (t60) cc_final: 0.7601 (t60) REVERT: C 443 LYS cc_start: 0.8824 (mmtt) cc_final: 0.8332 (mtpp) REVERT: C 453 GLU cc_start: 0.8445 (pp20) cc_final: 0.7971 (pp20) REVERT: C 457 ASN cc_start: 0.9178 (m110) cc_final: 0.8945 (m-40) REVERT: C 473 ASP cc_start: 0.8418 (p0) cc_final: 0.7779 (p0) REVERT: C 515 MET cc_start: 0.7031 (pp-130) cc_final: 0.6807 (pp-130) REVERT: D 439 TRP cc_start: 0.8126 (t60) cc_final: 0.7515 (t60) REVERT: D 443 LYS cc_start: 0.8878 (mmtt) cc_final: 0.8496 (mtpp) REVERT: D 453 GLU cc_start: 0.8430 (pp20) cc_final: 0.8020 (pp20) REVERT: D 457 ASN cc_start: 0.9228 (m110) cc_final: 0.8776 (m-40) REVERT: D 461 ASP cc_start: 0.8391 (t70) cc_final: 0.7975 (t70) REVERT: D 473 ASP cc_start: 0.8356 (p0) cc_final: 0.8079 (p0) REVERT: D 515 MET cc_start: 0.7345 (pp-130) cc_final: 0.6835 (pp-130) REVERT: E 439 TRP cc_start: 0.8012 (t60) cc_final: 0.7513 (t60) REVERT: E 443 LYS cc_start: 0.8830 (mmtt) cc_final: 0.8427 (mtpp) REVERT: E 453 GLU cc_start: 0.8454 (pp20) cc_final: 0.7940 (pp20) REVERT: E 457 ASN cc_start: 0.9099 (m110) cc_final: 0.8701 (m-40) REVERT: E 474 TYR cc_start: 0.7435 (t80) cc_final: 0.7157 (t80) REVERT: E 515 MET cc_start: 0.7228 (pp-130) cc_final: 0.6522 (pp-130) REVERT: G 439 TRP cc_start: 0.8114 (t60) cc_final: 0.7490 (t60) REVERT: G 443 LYS cc_start: 0.8837 (mmtt) cc_final: 0.8539 (mtpp) REVERT: G 447 ILE cc_start: 0.8654 (tt) cc_final: 0.8451 (tt) REVERT: G 458 GLN cc_start: 0.8563 (pt0) cc_final: 0.8120 (pt0) REVERT: G 515 MET cc_start: 0.7146 (pp-130) cc_final: 0.6766 (pp-130) REVERT: H 439 TRP cc_start: 0.8004 (t60) cc_final: 0.7528 (t60) REVERT: H 457 ASN cc_start: 0.9074 (m110) cc_final: 0.8322 (t0) REVERT: H 458 GLN cc_start: 0.8873 (pt0) cc_final: 0.8385 (pt0) REVERT: H 515 MET cc_start: 0.7211 (pp-130) cc_final: 0.6426 (pp-130) REVERT: I 439 TRP cc_start: 0.7832 (t60) cc_final: 0.7192 (t60) REVERT: I 443 LYS cc_start: 0.8784 (mmtt) cc_final: 0.8453 (mtpp) REVERT: I 457 ASN cc_start: 0.8943 (m110) cc_final: 0.8015 (t0) REVERT: I 458 GLN cc_start: 0.8856 (pt0) cc_final: 0.8642 (pt0) REVERT: I 474 TYR cc_start: 0.7834 (t80) cc_final: 0.7549 (t80) REVERT: I 515 MET cc_start: 0.7162 (pp-130) cc_final: 0.6416 (pp-130) REVERT: J 443 LYS cc_start: 0.8637 (mmtt) cc_final: 0.8283 (mtpp) REVERT: J 457 ASN cc_start: 0.9117 (m110) cc_final: 0.8299 (t0) REVERT: J 458 GLN cc_start: 0.8737 (pt0) cc_final: 0.8220 (pt0) REVERT: J 515 MET cc_start: 0.7266 (pp-130) cc_final: 0.6831 (pp-130) outliers start: 10 outliers final: 0 residues processed: 399 average time/residue: 0.2055 time to fit residues: 106.4627 Evaluate side-chains 335 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 489 GLN A 437 GLN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 GLN B 438 GLN B 489 GLN ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 GLN ** C 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 GLN ** D 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 489 GLN ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 489 GLN G 512 ASN G 514 GLN H 489 GLN H 512 ASN H 514 GLN ** I 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 489 GLN ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 489 GLN ** J 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.124541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.110600 restraints weight = 13580.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.114128 restraints weight = 7410.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.116588 restraints weight = 4657.369| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 6930 Z= 0.289 Angle : 0.879 9.654 9300 Z= 0.427 Chirality : 0.047 0.226 1100 Planarity : 0.003 0.014 1190 Dihedral : 6.470 16.837 900 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 4.68 % Allowed : 17.22 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.86 (0.21), residues: 840 helix: -4.31 (0.11), residues: 590 sheet: None (None), residues: 0 loop : -2.01 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 439 PHE 0.009 0.004 PHE H 501 TYR 0.008 0.002 TYR B 474 ARG 0.002 0.001 ARG J 488 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 362 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 439 TRP cc_start: 0.8073 (t60) cc_final: 0.7390 (t60) REVERT: F 443 LYS cc_start: 0.8845 (mmtt) cc_final: 0.8629 (mtpp) REVERT: F 444 ARG cc_start: 0.8937 (ttt180) cc_final: 0.8602 (ttt180) REVERT: F 450 GLN cc_start: 0.8449 (tm-30) cc_final: 0.8219 (tm-30) REVERT: F 451 MET cc_start: 0.8294 (tpp) cc_final: 0.8047 (tpt) REVERT: F 457 ASN cc_start: 0.9329 (m110) cc_final: 0.8899 (m-40) REVERT: F 460 LEU cc_start: 0.8883 (tt) cc_final: 0.8667 (tt) REVERT: F 474 TYR cc_start: 0.7506 (t80) cc_final: 0.6780 (t80) REVERT: F 515 MET cc_start: 0.6907 (OUTLIER) cc_final: 0.6382 (pp-130) REVERT: A 437 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.6674 (mt0) REVERT: A 441 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7414 (tm-30) REVERT: A 443 LYS cc_start: 0.8885 (mmtt) cc_final: 0.8520 (mmmt) REVERT: A 450 GLN cc_start: 0.8576 (tm-30) cc_final: 0.7824 (tm-30) REVERT: A 461 ASP cc_start: 0.8915 (t70) cc_final: 0.8440 (t70) REVERT: A 469 ILE cc_start: 0.9074 (tp) cc_final: 0.8833 (tt) REVERT: A 473 ASP cc_start: 0.8411 (p0) cc_final: 0.8099 (p0) REVERT: A 474 TYR cc_start: 0.7627 (t80) cc_final: 0.7174 (t80) REVERT: A 482 THR cc_start: 0.8168 (t) cc_final: 0.7809 (t) REVERT: A 500 GLU cc_start: 0.6914 (mp0) cc_final: 0.6657 (mp0) REVERT: B 443 LYS cc_start: 0.9077 (mmtt) cc_final: 0.8523 (tptp) REVERT: B 450 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8252 (tm-30) REVERT: B 457 ASN cc_start: 0.9177 (m110) cc_final: 0.8902 (m-40) REVERT: B 461 ASP cc_start: 0.8682 (t70) cc_final: 0.8477 (t70) REVERT: B 469 ILE cc_start: 0.9026 (tp) cc_final: 0.8636 (tt) REVERT: B 482 THR cc_start: 0.8172 (t) cc_final: 0.7809 (t) REVERT: B 500 GLU cc_start: 0.6219 (mp0) cc_final: 0.5934 (mp0) REVERT: B 515 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.6893 (pp-130) REVERT: C 440 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.9108 (mt) REVERT: C 450 GLN cc_start: 0.8603 (tm-30) cc_final: 0.7962 (tm-30) REVERT: C 458 GLN cc_start: 0.8598 (pt0) cc_final: 0.7986 (pt0) REVERT: C 469 ILE cc_start: 0.9030 (tp) cc_final: 0.8707 (tt) REVERT: C 482 THR cc_start: 0.8383 (t) cc_final: 0.8034 (t) REVERT: C 505 ILE cc_start: 0.8973 (tt) cc_final: 0.8709 (tt) REVERT: D 443 LYS cc_start: 0.8962 (mmtt) cc_final: 0.8238 (mmtt) REVERT: D 450 GLN cc_start: 0.8623 (tm-30) cc_final: 0.8255 (tm-30) REVERT: D 451 MET cc_start: 0.7937 (tpp) cc_final: 0.7680 (tpt) REVERT: D 457 ASN cc_start: 0.9399 (m110) cc_final: 0.9114 (m-40) REVERT: D 460 LEU cc_start: 0.8905 (tt) cc_final: 0.8583 (tt) REVERT: D 469 ILE cc_start: 0.9050 (tp) cc_final: 0.8756 (tt) REVERT: D 473 ASP cc_start: 0.8510 (p0) cc_final: 0.8154 (p0) REVERT: D 474 TYR cc_start: 0.7515 (t80) cc_final: 0.6765 (t80) REVERT: D 489 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8520 (mm-40) REVERT: D 515 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6642 (pp-130) REVERT: E 443 LYS cc_start: 0.8865 (mmtt) cc_final: 0.8577 (mmmt) REVERT: E 450 GLN cc_start: 0.8411 (tm-30) cc_final: 0.7934 (tm-30) REVERT: E 451 MET cc_start: 0.8098 (tpp) cc_final: 0.7856 (tpt) REVERT: E 458 GLN cc_start: 0.8329 (pt0) cc_final: 0.7841 (pt0) REVERT: E 474 TYR cc_start: 0.7654 (t80) cc_final: 0.7265 (t80) REVERT: E 500 GLU cc_start: 0.7120 (mp0) cc_final: 0.6853 (mp0) REVERT: E 515 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6700 (pp-130) REVERT: G 443 LYS cc_start: 0.8785 (mmtt) cc_final: 0.8539 (tptp) REVERT: G 474 TYR cc_start: 0.7647 (t80) cc_final: 0.7440 (t80) REVERT: H 515 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.6532 (pp-130) REVERT: I 443 LYS cc_start: 0.8814 (mmtt) cc_final: 0.8449 (tptp) REVERT: I 450 GLN cc_start: 0.8682 (tm-30) cc_final: 0.7954 (tm-30) REVERT: I 451 MET cc_start: 0.8435 (tpp) cc_final: 0.8036 (tpt) REVERT: I 482 THR cc_start: 0.8332 (t) cc_final: 0.7968 (t) REVERT: I 500 GLU cc_start: 0.6335 (mp0) cc_final: 0.6000 (mp0) REVERT: I 507 GLN cc_start: 0.7873 (pm20) cc_final: 0.7666 (pm20) REVERT: J 439 TRP cc_start: 0.8008 (t60) cc_final: 0.7355 (t60) REVERT: J 441 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7750 (mp10) REVERT: J 443 LYS cc_start: 0.8789 (mmtt) cc_final: 0.8559 (mtpp) REVERT: J 444 ARG cc_start: 0.9039 (ttt180) cc_final: 0.8720 (ttt180) REVERT: J 473 ASP cc_start: 0.8585 (p0) cc_final: 0.8237 (p0) REVERT: J 507 GLN cc_start: 0.7844 (pm20) cc_final: 0.7573 (pm20) REVERT: J 515 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6591 (pp-130) outliers start: 37 outliers final: 11 residues processed: 365 average time/residue: 0.2203 time to fit residues: 101.8277 Evaluate side-chains 353 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 331 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 515 MET Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 489 GLN Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 489 GLN Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 515 MET Chi-restraints excluded: chain H residue 515 MET Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain J residue 509 LEU Chi-restraints excluded: chain J residue 515 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 65 optimal weight: 20.0000 chunk 12 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 6 optimal weight: 0.3980 chunk 36 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 49 optimal weight: 20.0000 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 GLN B 489 GLN ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 GLN C 512 ASN C 514 GLN D 437 GLN D 489 GLN ** D 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 489 GLN ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 457 ASN H 489 GLN ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 512 ASN J 514 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.127857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.113478 restraints weight = 13510.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.117111 restraints weight = 7348.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.119557 restraints weight = 4615.538| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6930 Z= 0.216 Angle : 0.813 10.222 9300 Z= 0.383 Chirality : 0.045 0.133 1100 Planarity : 0.002 0.017 1190 Dihedral : 5.900 16.867 900 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 5.70 % Allowed : 17.09 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.70 (0.24), residues: 840 helix: -3.82 (0.13), residues: 570 sheet: None (None), residues: 0 loop : -0.78 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 439 PHE 0.010 0.003 PHE F 501 TYR 0.009 0.001 TYR B 474 ARG 0.002 0.000 ARG D 488 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 353 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 443 LYS cc_start: 0.8977 (mmtt) cc_final: 0.8600 (tptp) REVERT: F 444 ARG cc_start: 0.8926 (ttt180) cc_final: 0.8692 (ttt180) REVERT: F 450 GLN cc_start: 0.8332 (tm-30) cc_final: 0.8003 (tm-30) REVERT: F 451 MET cc_start: 0.8305 (tpp) cc_final: 0.8058 (tpp) REVERT: F 474 TYR cc_start: 0.7291 (t80) cc_final: 0.6779 (t80) REVERT: A 437 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.6620 (mt0) REVERT: A 441 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7181 (tm-30) REVERT: A 450 GLN cc_start: 0.8503 (tm-30) cc_final: 0.7779 (tm-30) REVERT: A 458 GLN cc_start: 0.8487 (pt0) cc_final: 0.8117 (pt0) REVERT: A 469 ILE cc_start: 0.9004 (tp) cc_final: 0.8761 (tt) REVERT: A 473 ASP cc_start: 0.8463 (p0) cc_final: 0.8043 (p0) REVERT: A 482 THR cc_start: 0.8097 (t) cc_final: 0.7728 (t) REVERT: B 441 GLN cc_start: 0.7783 (mp10) cc_final: 0.7524 (mp10) REVERT: B 450 GLN cc_start: 0.8421 (tm-30) cc_final: 0.8109 (tm-30) REVERT: B 451 MET cc_start: 0.8064 (tpt) cc_final: 0.7837 (tpt) REVERT: B 469 ILE cc_start: 0.9029 (tp) cc_final: 0.8666 (tt) REVERT: B 482 THR cc_start: 0.8143 (t) cc_final: 0.7779 (t) REVERT: B 515 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.6771 (pp-130) REVERT: B 517 LEU cc_start: 0.7620 (mt) cc_final: 0.7357 (mp) REVERT: C 443 LYS cc_start: 0.8914 (mmtt) cc_final: 0.8467 (mtpp) REVERT: C 450 GLN cc_start: 0.8490 (tm-30) cc_final: 0.7999 (tm-30) REVERT: C 451 MET cc_start: 0.8177 (tpt) cc_final: 0.7939 (tpt) REVERT: C 469 ILE cc_start: 0.8976 (tp) cc_final: 0.8689 (tt) REVERT: C 482 THR cc_start: 0.8326 (t) cc_final: 0.7997 (t) REVERT: C 505 ILE cc_start: 0.8873 (tt) cc_final: 0.8643 (tt) REVERT: D 450 GLN cc_start: 0.8474 (tm-30) cc_final: 0.8088 (tm-30) REVERT: D 461 ASP cc_start: 0.8871 (t70) cc_final: 0.8547 (t0) REVERT: D 469 ILE cc_start: 0.8965 (tp) cc_final: 0.8624 (tt) REVERT: D 473 ASP cc_start: 0.8552 (p0) cc_final: 0.8207 (p0) REVERT: D 474 TYR cc_start: 0.7419 (t80) cc_final: 0.6778 (t80) REVERT: D 507 GLN cc_start: 0.7488 (pm20) cc_final: 0.7214 (pm20) REVERT: D 515 MET cc_start: 0.6928 (OUTLIER) cc_final: 0.6285 (pp-130) REVERT: E 450 GLN cc_start: 0.8382 (tm-30) cc_final: 0.7882 (tm-30) REVERT: E 451 MET cc_start: 0.8152 (tpp) cc_final: 0.7915 (tpt) REVERT: E 500 GLU cc_start: 0.7281 (mp0) cc_final: 0.6965 (mp0) REVERT: E 515 MET cc_start: 0.7006 (OUTLIER) cc_final: 0.6414 (pp-130) REVERT: G 441 GLN cc_start: 0.8144 (mp10) cc_final: 0.7709 (mp10) REVERT: G 451 MET cc_start: 0.8119 (tpt) cc_final: 0.7911 (tpt) REVERT: G 458 GLN cc_start: 0.8735 (pt0) cc_final: 0.8324 (pt0) REVERT: H 450 GLN cc_start: 0.8823 (tm-30) cc_final: 0.8294 (tm-30) REVERT: H 451 MET cc_start: 0.8275 (tpt) cc_final: 0.7847 (tpt) REVERT: H 457 ASN cc_start: 0.8901 (m-40) cc_final: 0.8602 (m-40) REVERT: H 500 GLU cc_start: 0.6585 (mp0) cc_final: 0.6287 (mp0) REVERT: H 515 MET cc_start: 0.7116 (OUTLIER) cc_final: 0.6497 (pp-130) REVERT: I 451 MET cc_start: 0.8540 (tpp) cc_final: 0.8287 (tpt) REVERT: I 457 ASN cc_start: 0.8806 (m-40) cc_final: 0.8530 (m-40) REVERT: I 482 THR cc_start: 0.8254 (t) cc_final: 0.7913 (t) REVERT: I 500 GLU cc_start: 0.6530 (mp0) cc_final: 0.6171 (mp0) REVERT: I 507 GLN cc_start: 0.7904 (pm20) cc_final: 0.7696 (pm20) REVERT: J 441 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8128 (mp10) REVERT: J 443 LYS cc_start: 0.8831 (mmtt) cc_final: 0.8558 (tptp) REVERT: J 444 ARG cc_start: 0.9173 (ttt180) cc_final: 0.8962 (ttt180) REVERT: J 457 ASN cc_start: 0.8824 (m-40) cc_final: 0.8470 (m-40) REVERT: J 470 MET cc_start: 0.7279 (mtp) cc_final: 0.6947 (mtt) REVERT: J 473 ASP cc_start: 0.8543 (p0) cc_final: 0.8136 (p0) REVERT: J 500 GLU cc_start: 0.6133 (mp0) cc_final: 0.5880 (mp0) REVERT: J 507 GLN cc_start: 0.7888 (pm20) cc_final: 0.7682 (pm20) outliers start: 45 outliers final: 25 residues processed: 366 average time/residue: 0.2050 time to fit residues: 96.6426 Evaluate side-chains 370 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 338 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 509 LEU Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 515 MET Chi-restraints excluded: chain G residue 448 VAL Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain H residue 470 MET Chi-restraints excluded: chain H residue 491 LEU Chi-restraints excluded: chain H residue 515 MET Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 509 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 59 optimal weight: 0.0060 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 overall best weight: 3.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 457 ASN ** F 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 GLN ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 GLN D 437 GLN D 489 GLN ** D 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 457 ASN I 489 GLN ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.128082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.112926 restraints weight = 13578.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.116650 restraints weight = 7324.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.119262 restraints weight = 4590.897| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6930 Z= 0.210 Angle : 0.838 12.691 9300 Z= 0.380 Chirality : 0.044 0.131 1100 Planarity : 0.002 0.016 1190 Dihedral : 5.706 17.829 900 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 5.70 % Allowed : 19.87 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.76 (0.23), residues: 840 helix: -3.38 (0.15), residues: 590 sheet: None (None), residues: 0 loop : -1.92 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 439 PHE 0.012 0.004 PHE H 501 TYR 0.009 0.001 TYR B 474 ARG 0.003 0.001 ARG H 488 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 347 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 444 ARG cc_start: 0.9044 (ttt180) cc_final: 0.8717 (ttt180) REVERT: F 450 GLN cc_start: 0.8453 (tm-30) cc_final: 0.8136 (tm-30) REVERT: F 458 GLN cc_start: 0.8454 (pt0) cc_final: 0.8066 (pt0) REVERT: F 500 GLU cc_start: 0.6607 (mp0) cc_final: 0.6397 (mp0) REVERT: A 437 GLN cc_start: 0.7788 (mt0) cc_final: 0.6790 (mt0) REVERT: A 441 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7151 (tm-30) REVERT: A 450 GLN cc_start: 0.8516 (tm-30) cc_final: 0.7769 (tm-30) REVERT: A 469 ILE cc_start: 0.9005 (tp) cc_final: 0.8741 (tt) REVERT: A 473 ASP cc_start: 0.8446 (p0) cc_final: 0.7955 (p0) REVERT: A 482 THR cc_start: 0.8144 (t) cc_final: 0.7786 (t) REVERT: B 443 LYS cc_start: 0.8636 (mtpp) cc_final: 0.8294 (mtpp) REVERT: B 450 GLN cc_start: 0.8458 (tm-30) cc_final: 0.7678 (tm-30) REVERT: B 451 MET cc_start: 0.8145 (tpt) cc_final: 0.7624 (tpt) REVERT: B 458 GLN cc_start: 0.8463 (pt0) cc_final: 0.8242 (pt0) REVERT: B 469 ILE cc_start: 0.9072 (tp) cc_final: 0.8707 (tt) REVERT: B 482 THR cc_start: 0.8244 (t) cc_final: 0.7868 (t) REVERT: B 515 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.6829 (pp-130) REVERT: C 443 LYS cc_start: 0.8956 (mmtt) cc_final: 0.8356 (mtpp) REVERT: C 450 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8108 (tm-30) REVERT: C 458 GLN cc_start: 0.8339 (pt0) cc_final: 0.7462 (pt0) REVERT: C 469 ILE cc_start: 0.8955 (tp) cc_final: 0.8692 (tt) REVERT: C 482 THR cc_start: 0.8298 (t) cc_final: 0.7992 (t) REVERT: D 450 GLN cc_start: 0.8548 (tm-30) cc_final: 0.8192 (tm-30) REVERT: D 461 ASP cc_start: 0.8671 (t70) cc_final: 0.8358 (t0) REVERT: D 469 ILE cc_start: 0.8960 (tp) cc_final: 0.8636 (tt) REVERT: D 473 ASP cc_start: 0.8411 (p0) cc_final: 0.8062 (p0) REVERT: D 515 MET cc_start: 0.6781 (OUTLIER) cc_final: 0.6334 (pp-130) REVERT: E 450 GLN cc_start: 0.8507 (tm-30) cc_final: 0.7990 (tm-30) REVERT: E 451 MET cc_start: 0.8360 (tpp) cc_final: 0.7983 (tpt) REVERT: E 500 GLU cc_start: 0.7195 (mp0) cc_final: 0.6897 (mp0) REVERT: E 515 MET cc_start: 0.6775 (OUTLIER) cc_final: 0.6332 (pp-130) REVERT: G 444 ARG cc_start: 0.8721 (ttt180) cc_final: 0.8413 (ttt180) REVERT: G 450 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8173 (tm-30) REVERT: G 451 MET cc_start: 0.8381 (tpt) cc_final: 0.8100 (tpt) REVERT: G 458 GLN cc_start: 0.8711 (pt0) cc_final: 0.8342 (pt0) REVERT: H 450 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8253 (tm-30) REVERT: H 451 MET cc_start: 0.8261 (tpt) cc_final: 0.7786 (tpt) REVERT: H 457 ASN cc_start: 0.8731 (m-40) cc_final: 0.7850 (t0) REVERT: H 500 GLU cc_start: 0.6683 (mp0) cc_final: 0.6364 (mp0) REVERT: H 515 MET cc_start: 0.7050 (OUTLIER) cc_final: 0.6468 (pp-130) REVERT: H 517 LEU cc_start: 0.7406 (mp) cc_final: 0.7026 (mp) REVERT: I 457 ASN cc_start: 0.8808 (m-40) cc_final: 0.8506 (m-40) REVERT: I 482 THR cc_start: 0.8355 (t) cc_final: 0.8031 (t) REVERT: I 500 GLU cc_start: 0.6427 (mp0) cc_final: 0.6113 (mp0) REVERT: J 441 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8051 (mp10) REVERT: J 443 LYS cc_start: 0.8714 (mmtt) cc_final: 0.8464 (mtpp) REVERT: J 444 ARG cc_start: 0.9119 (ttt180) cc_final: 0.8858 (ttt180) REVERT: J 450 GLN cc_start: 0.8685 (tm-30) cc_final: 0.7994 (tm-30) REVERT: J 457 ASN cc_start: 0.8718 (m-40) cc_final: 0.8434 (m-40) REVERT: J 470 MET cc_start: 0.7094 (mtp) cc_final: 0.6832 (mtp) REVERT: J 473 ASP cc_start: 0.8496 (p0) cc_final: 0.7959 (p0) REVERT: J 500 GLU cc_start: 0.6223 (mp0) cc_final: 0.5943 (mp0) REVERT: J 507 GLN cc_start: 0.7888 (pm20) cc_final: 0.7674 (pm20) outliers start: 45 outliers final: 29 residues processed: 358 average time/residue: 0.2102 time to fit residues: 96.0062 Evaluate side-chains 377 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 342 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 509 LEU Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 489 GLN Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 489 GLN Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 515 MET Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 504 VAL Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain H residue 453 GLU Chi-restraints excluded: chain H residue 482 THR Chi-restraints excluded: chain H residue 491 LEU Chi-restraints excluded: chain H residue 515 MET Chi-restraints excluded: chain I residue 453 GLU Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain J residue 453 GLU Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 509 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 60 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 69 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 512 ASN F 514 GLN ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 GLN B 512 ASN B 514 GLN C 457 ASN C 489 GLN D 489 GLN ** E 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 457 ASN ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.128157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.114032 restraints weight = 13392.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.117545 restraints weight = 7424.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.120056 restraints weight = 4681.433| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6930 Z= 0.221 Angle : 0.843 11.227 9300 Z= 0.383 Chirality : 0.045 0.140 1100 Planarity : 0.003 0.018 1190 Dihedral : 5.663 16.085 900 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 6.46 % Allowed : 20.89 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.11 (0.26), residues: 840 helix: -3.02 (0.17), residues: 590 sheet: None (None), residues: 0 loop : -1.30 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 439 PHE 0.013 0.004 PHE B 501 TYR 0.007 0.001 TYR A 474 ARG 0.008 0.001 ARG J 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 349 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 441 GLN cc_start: 0.8303 (pm20) cc_final: 0.7779 (mp10) REVERT: F 444 ARG cc_start: 0.9053 (ttt180) cc_final: 0.8754 (ttt180) REVERT: F 445 GLU cc_start: 0.8172 (tp30) cc_final: 0.7775 (tp30) REVERT: F 450 GLN cc_start: 0.8596 (tm-30) cc_final: 0.8237 (tm-30) REVERT: F 451 MET cc_start: 0.8024 (tpt) cc_final: 0.7579 (tpt) REVERT: F 458 GLN cc_start: 0.8347 (pt0) cc_final: 0.8013 (pt0) REVERT: F 500 GLU cc_start: 0.6487 (mp0) cc_final: 0.6223 (mp0) REVERT: A 437 GLN cc_start: 0.7851 (mt0) cc_final: 0.6833 (mt0) REVERT: A 441 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7254 (tm-30) REVERT: A 443 LYS cc_start: 0.8820 (mtpt) cc_final: 0.8450 (mtpp) REVERT: A 450 GLN cc_start: 0.8596 (tm-30) cc_final: 0.7721 (tm-30) REVERT: A 458 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7587 (pt0) REVERT: A 469 ILE cc_start: 0.8961 (tp) cc_final: 0.8701 (tt) REVERT: A 473 ASP cc_start: 0.8532 (p0) cc_final: 0.8094 (p0) REVERT: A 482 THR cc_start: 0.8206 (t) cc_final: 0.7857 (t) REVERT: B 450 GLN cc_start: 0.8484 (tm-30) cc_final: 0.7665 (tm-30) REVERT: B 451 MET cc_start: 0.8151 (tpt) cc_final: 0.7614 (tpt) REVERT: B 458 GLN cc_start: 0.8442 (pt0) cc_final: 0.8161 (pt0) REVERT: B 469 ILE cc_start: 0.9071 (tp) cc_final: 0.8745 (tt) REVERT: B 482 THR cc_start: 0.7906 (t) cc_final: 0.7516 (t) REVERT: B 515 MET cc_start: 0.7240 (OUTLIER) cc_final: 0.6524 (pp-130) REVERT: B 517 LEU cc_start: 0.7302 (mp) cc_final: 0.6997 (mp) REVERT: C 443 LYS cc_start: 0.8952 (mmtt) cc_final: 0.8396 (mtpp) REVERT: C 450 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8132 (tm-30) REVERT: C 458 GLN cc_start: 0.8201 (pt0) cc_final: 0.7352 (pt0) REVERT: C 469 ILE cc_start: 0.8887 (tp) cc_final: 0.8624 (tt) REVERT: C 482 THR cc_start: 0.8283 (t) cc_final: 0.7981 (t) REVERT: D 444 ARG cc_start: 0.8931 (ttt180) cc_final: 0.8719 (ttt180) REVERT: D 445 GLU cc_start: 0.8483 (tp30) cc_final: 0.8008 (tp30) REVERT: D 450 GLN cc_start: 0.8479 (tm-30) cc_final: 0.7513 (tm-30) REVERT: D 469 ILE cc_start: 0.8966 (tp) cc_final: 0.8667 (tt) REVERT: D 473 ASP cc_start: 0.8487 (p0) cc_final: 0.8174 (p0) REVERT: D 500 GLU cc_start: 0.6749 (mp0) cc_final: 0.6538 (mp0) REVERT: D 515 MET cc_start: 0.6895 (OUTLIER) cc_final: 0.6349 (pp-130) REVERT: D 517 LEU cc_start: 0.7300 (mp) cc_final: 0.6985 (mp) REVERT: E 443 LYS cc_start: 0.8888 (mmmt) cc_final: 0.8640 (mtpp) REVERT: E 450 GLN cc_start: 0.8755 (tm-30) cc_final: 0.8189 (tm-30) REVERT: E 451 MET cc_start: 0.8421 (tpp) cc_final: 0.7968 (tpt) REVERT: E 470 MET cc_start: 0.7558 (mtp) cc_final: 0.7331 (mtp) REVERT: E 472 GLU cc_start: 0.6687 (OUTLIER) cc_final: 0.5986 (pp20) REVERT: E 500 GLU cc_start: 0.7153 (mp0) cc_final: 0.6868 (mp0) REVERT: E 515 MET cc_start: 0.7007 (OUTLIER) cc_final: 0.6538 (pp-130) REVERT: E 517 LEU cc_start: 0.7070 (mp) cc_final: 0.6854 (mp) REVERT: G 444 ARG cc_start: 0.8621 (ttt180) cc_final: 0.8233 (ttt180) REVERT: G 450 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8041 (tm-30) REVERT: G 451 MET cc_start: 0.8358 (tpt) cc_final: 0.7991 (tpt) REVERT: G 458 GLN cc_start: 0.8713 (pt0) cc_final: 0.8315 (pt0) REVERT: G 470 MET cc_start: 0.6956 (mtp) cc_final: 0.6520 (mtp) REVERT: H 450 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8188 (tm-30) REVERT: H 451 MET cc_start: 0.8248 (tpt) cc_final: 0.7667 (tpt) REVERT: H 457 ASN cc_start: 0.8815 (m-40) cc_final: 0.8072 (t0) REVERT: H 458 GLN cc_start: 0.8873 (pt0) cc_final: 0.8356 (pt0) REVERT: H 500 GLU cc_start: 0.6651 (mp0) cc_final: 0.6312 (mp0) REVERT: H 515 MET cc_start: 0.6968 (OUTLIER) cc_final: 0.6285 (pp-130) REVERT: I 450 GLN cc_start: 0.8638 (tm-30) cc_final: 0.7780 (tm-30) REVERT: I 457 ASN cc_start: 0.8763 (m-40) cc_final: 0.8496 (m-40) REVERT: I 469 ILE cc_start: 0.8785 (tp) cc_final: 0.8575 (tt) REVERT: I 470 MET cc_start: 0.7536 (mtp) cc_final: 0.7320 (mmm) REVERT: I 482 THR cc_start: 0.8459 (t) cc_final: 0.8218 (t) REVERT: I 500 GLU cc_start: 0.6451 (mp0) cc_final: 0.6097 (mp0) REVERT: J 441 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8103 (mp10) REVERT: J 443 LYS cc_start: 0.8792 (mmtt) cc_final: 0.8414 (mtpp) REVERT: J 444 ARG cc_start: 0.9133 (ttt180) cc_final: 0.8863 (ttt180) REVERT: J 450 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8081 (tm-30) REVERT: J 457 ASN cc_start: 0.8672 (m-40) cc_final: 0.8308 (t0) REVERT: J 470 MET cc_start: 0.7259 (mtp) cc_final: 0.6166 (ttm) REVERT: J 473 ASP cc_start: 0.8463 (p0) cc_final: 0.7846 (p0) REVERT: J 500 GLU cc_start: 0.6328 (mp0) cc_final: 0.6054 (mp0) REVERT: J 507 GLN cc_start: 0.7698 (pm20) cc_final: 0.7453 (pm20) outliers start: 51 outliers final: 35 residues processed: 364 average time/residue: 0.2175 time to fit residues: 100.7085 Evaluate side-chains 386 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 343 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 472 GLU Chi-restraints excluded: chain E residue 482 THR Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 515 MET Chi-restraints excluded: chain G residue 448 VAL Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain H residue 453 GLU Chi-restraints excluded: chain H residue 482 THR Chi-restraints excluded: chain H residue 491 LEU Chi-restraints excluded: chain H residue 515 MET Chi-restraints excluded: chain I residue 453 GLU Chi-restraints excluded: chain I residue 460 LEU Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain I residue 504 VAL Chi-restraints excluded: chain I residue 509 LEU Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain J residue 453 GLU Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 504 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 ASN ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 GLN C 489 GLN ** D 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 489 GLN ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 457 ASN ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 438 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.131966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.117150 restraints weight = 13374.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.120913 restraints weight = 7280.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.123555 restraints weight = 4565.005| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6930 Z= 0.172 Angle : 0.822 11.191 9300 Z= 0.370 Chirality : 0.043 0.141 1100 Planarity : 0.003 0.023 1190 Dihedral : 5.320 16.058 900 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 6.84 % Allowed : 19.87 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.26), residues: 840 helix: -2.70 (0.18), residues: 590 sheet: None (None), residues: 0 loop : -1.36 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 439 PHE 0.010 0.003 PHE B 501 TYR 0.007 0.001 TYR I 474 ARG 0.007 0.001 ARG H 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 362 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 441 GLN cc_start: 0.8056 (pm20) cc_final: 0.7575 (mp10) REVERT: F 445 GLU cc_start: 0.8170 (tp30) cc_final: 0.7863 (tp30) REVERT: F 450 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8300 (tm-30) REVERT: F 457 ASN cc_start: 0.8981 (m-40) cc_final: 0.8734 (m-40) REVERT: F 458 GLN cc_start: 0.8397 (pt0) cc_final: 0.8092 (pt0) REVERT: F 500 GLU cc_start: 0.6614 (mp0) cc_final: 0.6408 (mp0) REVERT: F 515 MET cc_start: 0.6643 (pp-130) cc_final: 0.6180 (pp-130) REVERT: A 437 GLN cc_start: 0.7882 (mt0) cc_final: 0.6916 (mt0) REVERT: A 441 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7366 (tm-30) REVERT: A 443 LYS cc_start: 0.8764 (mtpt) cc_final: 0.8390 (mtpp) REVERT: A 450 GLN cc_start: 0.8576 (tm-30) cc_final: 0.7797 (tm-30) REVERT: A 458 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.6954 (pt0) REVERT: A 469 ILE cc_start: 0.8938 (tp) cc_final: 0.8692 (tt) REVERT: A 473 ASP cc_start: 0.8478 (p0) cc_final: 0.8083 (p0) REVERT: A 482 THR cc_start: 0.8129 (t) cc_final: 0.7797 (t) REVERT: B 450 GLN cc_start: 0.8582 (tm-30) cc_final: 0.7837 (tm-30) REVERT: B 451 MET cc_start: 0.8141 (tpt) cc_final: 0.7823 (tpt) REVERT: B 461 ASP cc_start: 0.8970 (t70) cc_final: 0.8759 (t0) REVERT: B 469 ILE cc_start: 0.8976 (tp) cc_final: 0.8653 (tt) REVERT: B 482 THR cc_start: 0.8192 (t) cc_final: 0.7818 (t) REVERT: B 500 GLU cc_start: 0.6273 (mp0) cc_final: 0.6033 (mp0) REVERT: C 443 LYS cc_start: 0.8880 (mmtt) cc_final: 0.8170 (mttt) REVERT: C 450 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8134 (tm-30) REVERT: C 458 GLN cc_start: 0.8048 (pt0) cc_final: 0.7037 (pt0) REVERT: C 461 ASP cc_start: 0.8901 (t70) cc_final: 0.8566 (t0) REVERT: C 469 ILE cc_start: 0.8880 (tp) cc_final: 0.8664 (tt) REVERT: C 500 GLU cc_start: 0.6714 (mp0) cc_final: 0.6504 (mp0) REVERT: D 450 GLN cc_start: 0.8508 (tm-30) cc_final: 0.7531 (tm-30) REVERT: D 469 ILE cc_start: 0.8893 (tp) cc_final: 0.8586 (tt) REVERT: D 473 ASP cc_start: 0.8426 (p0) cc_final: 0.8144 (p0) REVERT: D 474 TYR cc_start: 0.7351 (t80) cc_final: 0.7135 (t80) REVERT: D 517 LEU cc_start: 0.7383 (mp) cc_final: 0.7040 (mp) REVERT: E 450 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8108 (tm-30) REVERT: E 451 MET cc_start: 0.8413 (tpp) cc_final: 0.7996 (tpt) REVERT: E 470 MET cc_start: 0.7470 (mtp) cc_final: 0.6623 (mtp) REVERT: E 472 GLU cc_start: 0.6616 (OUTLIER) cc_final: 0.6060 (pp20) REVERT: E 500 GLU cc_start: 0.7131 (mp0) cc_final: 0.6871 (mp0) REVERT: E 515 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6244 (pp-130) REVERT: E 517 LEU cc_start: 0.7248 (mp) cc_final: 0.6698 (mp) REVERT: G 444 ARG cc_start: 0.8523 (ttt180) cc_final: 0.8011 (ttt180) REVERT: G 450 GLN cc_start: 0.8678 (tm-30) cc_final: 0.7962 (tm-30) REVERT: G 451 MET cc_start: 0.8366 (tpt) cc_final: 0.8131 (tpt) REVERT: G 458 GLN cc_start: 0.8689 (pt0) cc_final: 0.8416 (pt0) REVERT: H 450 GLN cc_start: 0.8609 (tm-30) cc_final: 0.8309 (tm-30) REVERT: H 451 MET cc_start: 0.8317 (tpt) cc_final: 0.7718 (tpt) REVERT: H 457 ASN cc_start: 0.8731 (m-40) cc_final: 0.8270 (t0) REVERT: H 458 GLN cc_start: 0.8850 (pt0) cc_final: 0.8412 (pt0) REVERT: H 500 GLU cc_start: 0.6571 (mp0) cc_final: 0.6267 (mp0) REVERT: H 515 MET cc_start: 0.6769 (OUTLIER) cc_final: 0.6059 (pp-130) REVERT: I 450 GLN cc_start: 0.8597 (tm-30) cc_final: 0.7699 (tm-30) REVERT: I 457 ASN cc_start: 0.8686 (m-40) cc_final: 0.8026 (t0) REVERT: I 482 THR cc_start: 0.8392 (t) cc_final: 0.8159 (t) REVERT: I 500 GLU cc_start: 0.6758 (mp0) cc_final: 0.6238 (mp0) REVERT: J 441 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8096 (mp10) REVERT: J 443 LYS cc_start: 0.8740 (mmtt) cc_final: 0.8452 (mtpp) REVERT: J 444 ARG cc_start: 0.9078 (ttt180) cc_final: 0.8799 (ttt180) REVERT: J 451 MET cc_start: 0.8338 (tpt) cc_final: 0.7948 (tpt) REVERT: J 457 ASN cc_start: 0.8643 (m-40) cc_final: 0.8224 (t0) REVERT: J 470 MET cc_start: 0.7003 (mtp) cc_final: 0.6781 (mtp) REVERT: J 473 ASP cc_start: 0.8408 (p0) cc_final: 0.7881 (p0) REVERT: J 500 GLU cc_start: 0.6317 (mp0) cc_final: 0.6016 (mp0) outliers start: 54 outliers final: 34 residues processed: 370 average time/residue: 0.2142 time to fit residues: 100.6751 Evaluate side-chains 389 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 349 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 453 GLU Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain E residue 453 GLU Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 472 GLU Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 515 MET Chi-restraints excluded: chain G residue 448 VAL Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain G residue 504 VAL Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain H residue 453 GLU Chi-restraints excluded: chain H residue 482 THR Chi-restraints excluded: chain H residue 491 LEU Chi-restraints excluded: chain H residue 515 MET Chi-restraints excluded: chain I residue 453 GLU Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain I residue 504 VAL Chi-restraints excluded: chain I residue 509 LEU Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain J residue 453 GLU Chi-restraints excluded: chain J residue 460 LEU Chi-restraints excluded: chain J residue 509 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 57 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 76 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 GLN ** E 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 457 ASN ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.122240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.108501 restraints weight = 13684.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.112007 restraints weight = 7591.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.114410 restraints weight = 4790.156| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 6930 Z= 0.360 Angle : 0.961 11.604 9300 Z= 0.451 Chirality : 0.049 0.150 1100 Planarity : 0.003 0.022 1190 Dihedral : 5.984 16.027 900 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 21.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 6.96 % Allowed : 22.28 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.27), residues: 840 helix: -2.80 (0.18), residues: 570 sheet: None (None), residues: 0 loop : -1.00 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP I 439 PHE 0.021 0.006 PHE B 501 TYR 0.009 0.002 TYR B 474 ARG 0.008 0.001 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 357 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 445 GLU cc_start: 0.8278 (tp30) cc_final: 0.7898 (tp30) REVERT: F 450 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8309 (tm-30) REVERT: F 451 MET cc_start: 0.7848 (tpt) cc_final: 0.7373 (tpt) REVERT: F 453 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8212 (tm-30) REVERT: F 458 GLN cc_start: 0.8538 (pt0) cc_final: 0.7742 (pt0) REVERT: A 437 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.6741 (mt0) REVERT: A 441 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7185 (tm-30) REVERT: A 443 LYS cc_start: 0.8890 (mtpt) cc_final: 0.8556 (mtpp) REVERT: A 450 GLN cc_start: 0.8568 (tm-30) cc_final: 0.7624 (tm-30) REVERT: A 469 ILE cc_start: 0.9024 (tp) cc_final: 0.8685 (tt) REVERT: A 473 ASP cc_start: 0.8445 (p0) cc_final: 0.8183 (p0) REVERT: A 482 THR cc_start: 0.8504 (t) cc_final: 0.8136 (t) REVERT: A 501 PHE cc_start: 0.9054 (t80) cc_final: 0.8705 (t80) REVERT: B 450 GLN cc_start: 0.8523 (tm-30) cc_final: 0.7636 (tm-30) REVERT: B 451 MET cc_start: 0.8138 (tpt) cc_final: 0.7603 (tpt) REVERT: B 466 ARG cc_start: 0.8494 (mtm-85) cc_final: 0.8134 (mtm-85) REVERT: B 469 ILE cc_start: 0.9143 (tp) cc_final: 0.8890 (tt) REVERT: B 479 THR cc_start: 0.9190 (t) cc_final: 0.8987 (t) REVERT: B 482 THR cc_start: 0.8090 (t) cc_final: 0.7717 (t) REVERT: B 500 GLU cc_start: 0.6739 (mp0) cc_final: 0.6471 (mp0) REVERT: C 443 LYS cc_start: 0.8711 (mmtt) cc_final: 0.8410 (mtpp) REVERT: C 450 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8044 (tm-30) REVERT: C 458 GLN cc_start: 0.8266 (pt0) cc_final: 0.7238 (pt0) REVERT: C 469 ILE cc_start: 0.9084 (tp) cc_final: 0.8756 (tt) REVERT: C 488 ARG cc_start: 0.8639 (mtm180) cc_final: 0.8270 (mtm180) REVERT: D 450 GLN cc_start: 0.8478 (tm-30) cc_final: 0.8186 (tm-30) REVERT: D 469 ILE cc_start: 0.9015 (tp) cc_final: 0.8768 (tt) REVERT: E 444 ARG cc_start: 0.8940 (ttt180) cc_final: 0.8712 (ttt180) REVERT: E 450 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8247 (tm-30) REVERT: E 451 MET cc_start: 0.8398 (tpp) cc_final: 0.7893 (tpt) REVERT: E 470 MET cc_start: 0.7654 (mtp) cc_final: 0.7273 (mtp) REVERT: E 472 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6073 (pp20) REVERT: E 500 GLU cc_start: 0.7343 (mp0) cc_final: 0.7082 (mp0) REVERT: E 515 MET cc_start: 0.6677 (OUTLIER) cc_final: 0.6259 (pp-130) REVERT: G 450 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8171 (tm-30) REVERT: G 451 MET cc_start: 0.8456 (tpt) cc_final: 0.7987 (tpt) REVERT: G 458 GLN cc_start: 0.8749 (pt0) cc_final: 0.8458 (pt0) REVERT: G 470 MET cc_start: 0.7671 (mtp) cc_final: 0.6978 (mtp) REVERT: H 450 GLN cc_start: 0.8709 (tm-30) cc_final: 0.8331 (tm-30) REVERT: H 451 MET cc_start: 0.8479 (tpt) cc_final: 0.7860 (tpt) REVERT: H 457 ASN cc_start: 0.8917 (m-40) cc_final: 0.8080 (t0) REVERT: H 458 GLN cc_start: 0.8957 (pt0) cc_final: 0.8481 (pt0) REVERT: I 450 GLN cc_start: 0.8638 (tm-30) cc_final: 0.7961 (tm-30) REVERT: I 457 ASN cc_start: 0.8857 (m-40) cc_final: 0.8588 (m-40) REVERT: I 473 ASP cc_start: 0.8581 (p0) cc_final: 0.8309 (p0) REVERT: I 500 GLU cc_start: 0.7023 (mp0) cc_final: 0.6605 (mp0) REVERT: I 515 MET cc_start: 0.6599 (pp-130) cc_final: 0.5960 (pp-130) REVERT: I 517 LEU cc_start: 0.6862 (mp) cc_final: 0.6382 (mp) REVERT: J 441 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8282 (mp10) REVERT: J 443 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8508 (mtpp) REVERT: J 444 ARG cc_start: 0.9111 (ttt180) cc_final: 0.8839 (ttt180) REVERT: J 450 GLN cc_start: 0.8758 (tm-30) cc_final: 0.7878 (tm-30) REVERT: J 451 MET cc_start: 0.8261 (tpt) cc_final: 0.7801 (tpt) REVERT: J 457 ASN cc_start: 0.8816 (m-40) cc_final: 0.8493 (m-40) REVERT: J 470 MET cc_start: 0.7407 (mtp) cc_final: 0.6678 (mtp) REVERT: J 473 ASP cc_start: 0.8465 (p0) cc_final: 0.7972 (p0) REVERT: J 500 GLU cc_start: 0.6315 (mp0) cc_final: 0.6012 (mp0) outliers start: 55 outliers final: 39 residues processed: 371 average time/residue: 0.2073 time to fit residues: 98.1105 Evaluate side-chains 385 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 340 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 447 ILE Chi-restraints excluded: chain F residue 453 GLU Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 472 GLU Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 515 MET Chi-restraints excluded: chain G residue 448 VAL Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain H residue 453 GLU Chi-restraints excluded: chain H residue 482 THR Chi-restraints excluded: chain H residue 509 LEU Chi-restraints excluded: chain I residue 453 GLU Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain I residue 504 VAL Chi-restraints excluded: chain I residue 509 LEU Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain J residue 447 ILE Chi-restraints excluded: chain J residue 453 GLU Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 509 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 27 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 77 optimal weight: 0.0970 chunk 18 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 438 GLN A 438 GLN ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 438 GLN ** E 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 438 GLN H 438 GLN I 438 GLN ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.127318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.113125 restraints weight = 13571.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.116745 restraints weight = 7566.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.119263 restraints weight = 4763.424| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.5633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6930 Z= 0.235 Angle : 0.949 12.123 9300 Z= 0.431 Chirality : 0.047 0.186 1100 Planarity : 0.003 0.039 1190 Dihedral : 5.688 18.589 900 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 5.82 % Allowed : 24.94 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.28), residues: 840 helix: -2.63 (0.19), residues: 530 sheet: None (None), residues: 0 loop : -1.08 (0.38), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP I 439 PHE 0.029 0.004 PHE B 501 TYR 0.009 0.002 TYR I 474 ARG 0.008 0.001 ARG E 466 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 357 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 438 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8313 (pt0) REVERT: F 445 GLU cc_start: 0.8142 (tp30) cc_final: 0.7934 (tp30) REVERT: F 450 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8347 (tm-30) REVERT: F 451 MET cc_start: 0.7931 (tpt) cc_final: 0.7548 (tpt) REVERT: F 457 ASN cc_start: 0.8983 (m-40) cc_final: 0.8778 (m110) REVERT: F 458 GLN cc_start: 0.8425 (pt0) cc_final: 0.7704 (pt0) REVERT: F 482 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8487 (t) REVERT: A 437 GLN cc_start: 0.7903 (mt0) cc_final: 0.6804 (mt0) REVERT: A 441 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.6867 (tm-30) REVERT: A 443 LYS cc_start: 0.8757 (mtpt) cc_final: 0.8450 (mtpp) REVERT: A 450 GLN cc_start: 0.8638 (tm-30) cc_final: 0.7724 (tm-30) REVERT: A 469 ILE cc_start: 0.8934 (tp) cc_final: 0.8635 (tt) REVERT: A 473 ASP cc_start: 0.8463 (p0) cc_final: 0.8050 (p0) REVERT: A 482 THR cc_start: 0.8378 (t) cc_final: 0.8041 (t) REVERT: A 501 PHE cc_start: 0.9010 (t80) cc_final: 0.8800 (t80) REVERT: B 450 GLN cc_start: 0.8533 (tm-30) cc_final: 0.7735 (tm-30) REVERT: B 451 MET cc_start: 0.8139 (tpt) cc_final: 0.7621 (tpt) REVERT: B 458 GLN cc_start: 0.8499 (pt0) cc_final: 0.8204 (pt0) REVERT: B 466 ARG cc_start: 0.8415 (mtm-85) cc_final: 0.8206 (mpp80) REVERT: B 469 ILE cc_start: 0.9064 (tp) cc_final: 0.8727 (tt) REVERT: B 482 THR cc_start: 0.7977 (t) cc_final: 0.7591 (t) REVERT: B 500 GLU cc_start: 0.6874 (mp0) cc_final: 0.6594 (mp0) REVERT: C 443 LYS cc_start: 0.8702 (mmtt) cc_final: 0.8397 (mtpp) REVERT: C 450 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8130 (tm-30) REVERT: C 458 GLN cc_start: 0.8207 (pt0) cc_final: 0.7296 (pt0) REVERT: C 469 ILE cc_start: 0.9031 (tp) cc_final: 0.8704 (tt) REVERT: C 482 THR cc_start: 0.8326 (OUTLIER) cc_final: 0.8050 (t) REVERT: C 488 ARG cc_start: 0.8484 (mtm180) cc_final: 0.8058 (mtm180) REVERT: C 501 PHE cc_start: 0.8913 (t80) cc_final: 0.8700 (t80) REVERT: D 444 ARG cc_start: 0.8874 (ttt180) cc_final: 0.8550 (ttt180) REVERT: D 450 GLN cc_start: 0.8535 (tm-30) cc_final: 0.7414 (tm-30) REVERT: D 461 ASP cc_start: 0.8772 (t70) cc_final: 0.8485 (t0) REVERT: D 469 ILE cc_start: 0.9010 (tp) cc_final: 0.8739 (tt) REVERT: E 443 LYS cc_start: 0.8446 (mtpp) cc_final: 0.8016 (ptpt) REVERT: E 450 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8124 (tm-30) REVERT: E 451 MET cc_start: 0.8382 (tpp) cc_final: 0.7985 (tpt) REVERT: E 470 MET cc_start: 0.7546 (mtp) cc_final: 0.7211 (mtp) REVERT: E 472 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6068 (pp20) REVERT: E 482 THR cc_start: 0.8419 (t) cc_final: 0.8050 (t) REVERT: E 500 GLU cc_start: 0.7298 (mp0) cc_final: 0.7035 (mp0) REVERT: E 515 MET cc_start: 0.6535 (OUTLIER) cc_final: 0.6181 (pp-130) REVERT: G 444 ARG cc_start: 0.8470 (ttt180) cc_final: 0.8206 (ttt180) REVERT: G 450 GLN cc_start: 0.8821 (tm-30) cc_final: 0.7794 (tm-30) REVERT: G 451 MET cc_start: 0.8384 (tpt) cc_final: 0.7985 (tpt) REVERT: G 458 GLN cc_start: 0.8770 (pt0) cc_final: 0.8454 (pt0) REVERT: H 450 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8397 (tm-30) REVERT: H 451 MET cc_start: 0.8427 (tpt) cc_final: 0.7770 (tpt) REVERT: H 457 ASN cc_start: 0.8803 (m-40) cc_final: 0.8151 (t0) REVERT: H 458 GLN cc_start: 0.8890 (pt0) cc_final: 0.8402 (pt0) REVERT: H 500 GLU cc_start: 0.6784 (mp0) cc_final: 0.6458 (mp0) REVERT: I 450 GLN cc_start: 0.8647 (tm-30) cc_final: 0.7843 (tm-30) REVERT: I 457 ASN cc_start: 0.8781 (m-40) cc_final: 0.8504 (m-40) REVERT: I 473 ASP cc_start: 0.8567 (p0) cc_final: 0.8286 (p0) REVERT: I 488 ARG cc_start: 0.8740 (mtm180) cc_final: 0.8481 (mtm180) REVERT: I 500 GLU cc_start: 0.7209 (mp0) cc_final: 0.6701 (mp0) REVERT: I 515 MET cc_start: 0.6622 (pp-130) cc_final: 0.6072 (pp-130) REVERT: I 517 LEU cc_start: 0.6937 (mp) cc_final: 0.6494 (mp) REVERT: J 441 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8228 (mp10) REVERT: J 443 LYS cc_start: 0.8700 (mmtt) cc_final: 0.8417 (mtpp) REVERT: J 450 GLN cc_start: 0.8833 (tm-30) cc_final: 0.7959 (tm-30) REVERT: J 451 MET cc_start: 0.8171 (tpt) cc_final: 0.7419 (ttt) REVERT: J 457 ASN cc_start: 0.8717 (m-40) cc_final: 0.8045 (t0) REVERT: J 470 MET cc_start: 0.7382 (mtp) cc_final: 0.6439 (mtp) REVERT: J 473 ASP cc_start: 0.8367 (p0) cc_final: 0.7893 (p0) REVERT: J 500 GLU cc_start: 0.6392 (mp0) cc_final: 0.6122 (mp0) outliers start: 46 outliers final: 34 residues processed: 371 average time/residue: 0.2174 time to fit residues: 102.5988 Evaluate side-chains 388 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 347 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 438 GLN Chi-restraints excluded: chain F residue 447 ILE Chi-restraints excluded: chain F residue 453 GLU Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 509 LEU Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain E residue 438 GLN Chi-restraints excluded: chain E residue 472 GLU Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 509 LEU Chi-restraints excluded: chain E residue 515 MET Chi-restraints excluded: chain G residue 448 VAL Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain H residue 453 GLU Chi-restraints excluded: chain H residue 460 LEU Chi-restraints excluded: chain H residue 482 THR Chi-restraints excluded: chain H residue 509 LEU Chi-restraints excluded: chain I residue 453 GLU Chi-restraints excluded: chain I residue 509 LEU Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain J residue 453 GLU Chi-restraints excluded: chain J residue 509 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 28 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 438 GLN ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 438 GLN ** E 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.130253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.115947 restraints weight = 13415.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.119649 restraints weight = 7389.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.122194 restraints weight = 4619.658| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.5812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6930 Z= 0.217 Angle : 0.960 12.910 9300 Z= 0.433 Chirality : 0.046 0.161 1100 Planarity : 0.003 0.046 1190 Dihedral : 5.535 17.969 900 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 5.44 % Allowed : 26.08 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.27), residues: 840 helix: -2.37 (0.19), residues: 590 sheet: None (None), residues: 0 loop : -1.93 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 439 PHE 0.026 0.004 PHE B 501 TYR 0.008 0.001 TYR I 474 ARG 0.009 0.001 ARG C 483 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 347 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 445 GLU cc_start: 0.8316 (tp30) cc_final: 0.7931 (pm20) REVERT: F 450 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8390 (tm-30) REVERT: F 451 MET cc_start: 0.7946 (tpt) cc_final: 0.7612 (tpt) REVERT: F 458 GLN cc_start: 0.8435 (pt0) cc_final: 0.8025 (pt0) REVERT: F 482 THR cc_start: 0.8748 (t) cc_final: 0.8445 (t) REVERT: F 488 ARG cc_start: 0.8962 (ttm170) cc_final: 0.8712 (mtm180) REVERT: F 500 GLU cc_start: 0.6493 (mp0) cc_final: 0.6262 (mm-30) REVERT: A 437 GLN cc_start: 0.7988 (mt0) cc_final: 0.6909 (mt0) REVERT: A 441 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.6895 (tm-30) REVERT: A 443 LYS cc_start: 0.8790 (mtpt) cc_final: 0.8487 (mtpp) REVERT: A 450 GLN cc_start: 0.8732 (tm-30) cc_final: 0.7762 (tm-30) REVERT: A 473 ASP cc_start: 0.8455 (p0) cc_final: 0.8120 (p0) REVERT: A 482 THR cc_start: 0.8320 (t) cc_final: 0.7995 (t) REVERT: A 515 MET cc_start: 0.7019 (pp-130) cc_final: 0.6112 (pp-130) REVERT: B 437 GLN cc_start: 0.6757 (mt0) cc_final: 0.6270 (mm-40) REVERT: B 441 GLN cc_start: 0.7756 (mp10) cc_final: 0.7023 (tp40) REVERT: B 450 GLN cc_start: 0.8493 (tm-30) cc_final: 0.7778 (tm-30) REVERT: B 451 MET cc_start: 0.8297 (tpt) cc_final: 0.7812 (tpt) REVERT: B 469 ILE cc_start: 0.9009 (tp) cc_final: 0.8667 (tt) REVERT: B 482 THR cc_start: 0.7836 (t) cc_final: 0.7453 (t) REVERT: B 500 GLU cc_start: 0.7000 (mp0) cc_final: 0.6718 (mp0) REVERT: C 443 LYS cc_start: 0.8659 (mmtt) cc_final: 0.8355 (mtpp) REVERT: C 450 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8314 (tm-30) REVERT: C 457 ASN cc_start: 0.8652 (m-40) cc_final: 0.8364 (m-40) REVERT: C 458 GLN cc_start: 0.8179 (pt0) cc_final: 0.7195 (pt0) REVERT: C 469 ILE cc_start: 0.8965 (tp) cc_final: 0.8678 (tt) REVERT: C 488 ARG cc_start: 0.8492 (mtm180) cc_final: 0.8087 (mtm180) REVERT: D 450 GLN cc_start: 0.8512 (tm-30) cc_final: 0.7469 (tm-30) REVERT: E 443 LYS cc_start: 0.8428 (mtpp) cc_final: 0.7993 (ptpt) REVERT: E 450 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8084 (tm-30) REVERT: E 451 MET cc_start: 0.8391 (tpp) cc_final: 0.7969 (tpt) REVERT: E 470 MET cc_start: 0.7506 (mtp) cc_final: 0.7167 (mtp) REVERT: E 472 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.5968 (pp20) REVERT: E 500 GLU cc_start: 0.7158 (mp0) cc_final: 0.6899 (mp0) REVERT: E 515 MET cc_start: 0.6675 (OUTLIER) cc_final: 0.6169 (pp-130) REVERT: G 450 GLN cc_start: 0.8751 (tm-30) cc_final: 0.7931 (tm-30) REVERT: G 451 MET cc_start: 0.8366 (tpt) cc_final: 0.8136 (tpt) REVERT: G 458 GLN cc_start: 0.8691 (pt0) cc_final: 0.8370 (pt0) REVERT: G 470 MET cc_start: 0.7404 (mtp) cc_final: 0.6711 (mtp) REVERT: H 450 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8400 (tm-30) REVERT: H 451 MET cc_start: 0.8417 (tpt) cc_final: 0.7668 (tpt) REVERT: H 457 ASN cc_start: 0.8863 (m-40) cc_final: 0.8148 (t0) REVERT: H 458 GLN cc_start: 0.8880 (pt0) cc_final: 0.8399 (pt0) REVERT: H 500 GLU cc_start: 0.6768 (mp0) cc_final: 0.6434 (mp0) REVERT: I 450 GLN cc_start: 0.8738 (tm-30) cc_final: 0.7955 (tm-30) REVERT: I 457 ASN cc_start: 0.8763 (m-40) cc_final: 0.8482 (m-40) REVERT: I 473 ASP cc_start: 0.8546 (p0) cc_final: 0.8247 (p0) REVERT: I 500 GLU cc_start: 0.7087 (mp0) cc_final: 0.6627 (mp0) REVERT: I 515 MET cc_start: 0.6587 (pp-130) cc_final: 0.6063 (pp-130) REVERT: I 517 LEU cc_start: 0.6855 (mp) cc_final: 0.6438 (mp) REVERT: J 441 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8283 (mp10) REVERT: J 443 LYS cc_start: 0.8656 (mmtt) cc_final: 0.8395 (mtpp) REVERT: J 444 ARG cc_start: 0.9009 (ttt180) cc_final: 0.8448 (ttt90) REVERT: J 450 GLN cc_start: 0.8817 (tm-30) cc_final: 0.7918 (tm-30) REVERT: J 451 MET cc_start: 0.8057 (tpt) cc_final: 0.7430 (ttt) REVERT: J 457 ASN cc_start: 0.8674 (m-40) cc_final: 0.8243 (t0) REVERT: J 500 GLU cc_start: 0.6454 (mp0) cc_final: 0.6163 (mp0) outliers start: 43 outliers final: 34 residues processed: 355 average time/residue: 0.1992 time to fit residues: 91.1095 Evaluate side-chains 374 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 336 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 447 ILE Chi-restraints excluded: chain F residue 453 GLU Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 458 GLN Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain E residue 472 GLU Chi-restraints excluded: chain E residue 509 LEU Chi-restraints excluded: chain E residue 515 MET Chi-restraints excluded: chain G residue 448 VAL Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain H residue 453 GLU Chi-restraints excluded: chain H residue 460 LEU Chi-restraints excluded: chain H residue 482 THR Chi-restraints excluded: chain H residue 509 LEU Chi-restraints excluded: chain I residue 448 VAL Chi-restraints excluded: chain I residue 453 GLU Chi-restraints excluded: chain I residue 504 VAL Chi-restraints excluded: chain I residue 509 LEU Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain J residue 453 GLU Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 509 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 67 optimal weight: 0.0470 chunk 1 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 11 optimal weight: 0.0170 chunk 48 optimal weight: 7.9990 chunk 47 optimal weight: 0.4980 overall best weight: 1.1120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 438 GLN F 457 ASN ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 514 GLN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 514 GLN ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.134931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.120135 restraints weight = 13529.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.123966 restraints weight = 7377.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.126689 restraints weight = 4596.366| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.6053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6930 Z= 0.214 Angle : 0.974 13.610 9300 Z= 0.439 Chirality : 0.045 0.157 1100 Planarity : 0.004 0.040 1190 Dihedral : 5.370 17.989 900 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 5.19 % Allowed : 27.09 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.27), residues: 840 helix: -2.27 (0.20), residues: 550 sheet: None (None), residues: 0 loop : -1.92 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 439 PHE 0.025 0.004 PHE B 501 TYR 0.009 0.001 TYR I 474 ARG 0.011 0.001 ARG D 483 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 338 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 443 LYS cc_start: 0.8678 (ptpt) cc_final: 0.8210 (ptpp) REVERT: F 445 GLU cc_start: 0.8174 (tp30) cc_final: 0.7653 (pm20) REVERT: F 450 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8350 (tm-30) REVERT: F 451 MET cc_start: 0.7974 (tpt) cc_final: 0.7668 (tpt) REVERT: F 458 GLN cc_start: 0.8365 (pt0) cc_final: 0.8021 (pt0) REVERT: F 482 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8277 (t) REVERT: F 488 ARG cc_start: 0.8902 (ttm170) cc_final: 0.8542 (mtm180) REVERT: F 500 GLU cc_start: 0.6600 (mp0) cc_final: 0.6300 (mm-30) REVERT: F 515 MET cc_start: 0.7246 (pp-130) cc_final: 0.6302 (pp-130) REVERT: A 437 GLN cc_start: 0.7672 (mt0) cc_final: 0.6883 (mt0) REVERT: A 441 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.6889 (tm-30) REVERT: A 443 LYS cc_start: 0.8763 (mtpt) cc_final: 0.8452 (mtpp) REVERT: A 450 GLN cc_start: 0.8580 (tm-30) cc_final: 0.7818 (tm-30) REVERT: A 458 GLN cc_start: 0.7830 (pt0) cc_final: 0.6957 (pt0) REVERT: A 469 ILE cc_start: 0.8855 (tp) cc_final: 0.8584 (tt) REVERT: A 473 ASP cc_start: 0.8466 (p0) cc_final: 0.8124 (p0) REVERT: A 482 THR cc_start: 0.8225 (t) cc_final: 0.7924 (t) REVERT: A 515 MET cc_start: 0.6934 (pp-130) cc_final: 0.5943 (pp-130) REVERT: B 441 GLN cc_start: 0.7752 (mp10) cc_final: 0.7049 (tp40) REVERT: B 450 GLN cc_start: 0.8453 (tm-30) cc_final: 0.8186 (tm-30) REVERT: B 451 MET cc_start: 0.8299 (tpt) cc_final: 0.8094 (tpt) REVERT: B 458 GLN cc_start: 0.8407 (pt0) cc_final: 0.8150 (pt0) REVERT: B 469 ILE cc_start: 0.8911 (tp) cc_final: 0.8615 (tt) REVERT: B 482 THR cc_start: 0.8193 (t) cc_final: 0.7830 (t) REVERT: B 500 GLU cc_start: 0.6805 (mp0) cc_final: 0.6524 (mp0) REVERT: C 443 LYS cc_start: 0.8577 (mmtt) cc_final: 0.8250 (mtpp) REVERT: C 450 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8153 (tm-30) REVERT: C 457 ASN cc_start: 0.8532 (m-40) cc_final: 0.8109 (m-40) REVERT: C 458 GLN cc_start: 0.7852 (pt0) cc_final: 0.6854 (pt0) REVERT: C 469 ILE cc_start: 0.8803 (tp) cc_final: 0.8582 (tt) REVERT: C 488 ARG cc_start: 0.8455 (mtm180) cc_final: 0.8014 (mtm180) REVERT: D 450 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8265 (tm-30) REVERT: D 461 ASP cc_start: 0.8759 (t0) cc_final: 0.8485 (t0) REVERT: E 443 LYS cc_start: 0.8294 (mtpp) cc_final: 0.8001 (ptpt) REVERT: E 450 GLN cc_start: 0.8615 (tm-30) cc_final: 0.7980 (tm-30) REVERT: E 451 MET cc_start: 0.8290 (tpp) cc_final: 0.7867 (tpt) REVERT: E 472 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.5989 (pp20) REVERT: E 482 THR cc_start: 0.8324 (t) cc_final: 0.8055 (t) REVERT: E 500 GLU cc_start: 0.7097 (mp0) cc_final: 0.6850 (mp0) REVERT: E 515 MET cc_start: 0.6633 (OUTLIER) cc_final: 0.6017 (pp-130) REVERT: G 450 GLN cc_start: 0.8717 (tm-30) cc_final: 0.8068 (tm-30) REVERT: G 451 MET cc_start: 0.8273 (tpt) cc_final: 0.8013 (tpt) REVERT: G 470 MET cc_start: 0.7373 (mtp) cc_final: 0.6684 (mtp) REVERT: H 450 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8255 (tm-30) REVERT: H 451 MET cc_start: 0.8468 (tpt) cc_final: 0.7655 (tpt) REVERT: H 457 ASN cc_start: 0.8879 (m-40) cc_final: 0.8362 (t0) REVERT: H 458 GLN cc_start: 0.8876 (pt0) cc_final: 0.8397 (pt0) REVERT: H 500 GLU cc_start: 0.6849 (mp0) cc_final: 0.6597 (mp0) REVERT: I 450 GLN cc_start: 0.8673 (tm-30) cc_final: 0.7831 (tm-30) REVERT: I 457 ASN cc_start: 0.8776 (m-40) cc_final: 0.8007 (t0) REVERT: I 482 THR cc_start: 0.8396 (t) cc_final: 0.8043 (t) REVERT: I 500 GLU cc_start: 0.6886 (mp0) cc_final: 0.6408 (mp0) REVERT: I 515 MET cc_start: 0.6758 (pp-130) cc_final: 0.6087 (pp-130) REVERT: I 517 LEU cc_start: 0.7016 (mp) cc_final: 0.6608 (mp) REVERT: J 443 LYS cc_start: 0.8626 (mmtt) cc_final: 0.8350 (mtpp) REVERT: J 451 MET cc_start: 0.8108 (tpt) cc_final: 0.7682 (ttt) REVERT: J 457 ASN cc_start: 0.8629 (m-40) cc_final: 0.8227 (t0) REVERT: J 473 ASP cc_start: 0.8217 (p0) cc_final: 0.7793 (p0) REVERT: J 500 GLU cc_start: 0.6354 (mp0) cc_final: 0.5967 (mp0) outliers start: 41 outliers final: 34 residues processed: 346 average time/residue: 0.2057 time to fit residues: 91.2838 Evaluate side-chains 365 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 327 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 458 GLN Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain E residue 472 GLU Chi-restraints excluded: chain E residue 509 LEU Chi-restraints excluded: chain E residue 515 MET Chi-restraints excluded: chain G residue 448 VAL Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain H residue 453 GLU Chi-restraints excluded: chain H residue 460 LEU Chi-restraints excluded: chain H residue 482 THR Chi-restraints excluded: chain H residue 491 LEU Chi-restraints excluded: chain H residue 509 LEU Chi-restraints excluded: chain I residue 448 VAL Chi-restraints excluded: chain I residue 453 GLU Chi-restraints excluded: chain I residue 470 MET Chi-restraints excluded: chain I residue 509 LEU Chi-restraints excluded: chain J residue 453 GLU Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 509 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 74 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 457 ASN ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 514 GLN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 457 ASN ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.130715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.116497 restraints weight = 13548.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.120164 restraints weight = 7285.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.122652 restraints weight = 4554.428| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.6033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6930 Z= 0.263 Angle : 0.999 13.020 9300 Z= 0.457 Chirality : 0.047 0.182 1100 Planarity : 0.004 0.052 1190 Dihedral : 5.470 17.301 900 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.56 % Allowed : 28.35 % Favored : 67.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.28), residues: 840 helix: -2.24 (0.20), residues: 570 sheet: None (None), residues: 0 loop : -1.11 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 439 PHE 0.026 0.005 PHE B 501 TYR 0.011 0.002 TYR D 474 ARG 0.012 0.001 ARG C 483 =============================================================================== Job complete usr+sys time: 2287.88 seconds wall clock time: 42 minutes 0.21 seconds (2520.21 seconds total)