Starting phenix.real_space_refine on Tue Mar 11 21:36:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ggs_4399/03_2025/6ggs_4399.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ggs_4399/03_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_4399/03_2025/6ggs_4399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ggs_4399/03_2025/6ggs_4399.map" model { file = "/net/cci-nas-00/data/ceres_data/6ggs_4399/03_2025/6ggs_4399.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ggs_4399/03_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-5624/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: 2.36, per 1000 atoms: 0.34 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: 1.62 Conformation dependent library (CDL) restraints added in 991.6 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: 1.93 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 16.780 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.410 ------------------------------------------------------------------------------- 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 : 0.850 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: 0.1935 time to fit residues: 99.7561 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 : 0.855 ------------------------------------------------------------------------------- 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 = 33)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.110600 restraints weight = 13580.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.114164 restraints weight = 7410.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.116614 restraints weight = 4647.870| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 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 : 0.952 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: 0.7392 (t60) REVERT: F 443 LYS cc_start: 0.8845 (mmtt) cc_final: 0.8629 (mtpp) REVERT: F 444 ARG cc_start: 0.8936 (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: 0.8295 (tpp) cc_final: 0.8049 (tpt) REVERT: F 457 ASN cc_start: 0.9328 (m110) cc_final: 0.8899 (m-40) REVERT: F 460 LEU cc_start: 0.8884 (tt) cc_final: 0.8668 (tt) REVERT: F 474 TYR cc_start: 0.7508 (t80) cc_final: 0.6779 (t80) REVERT: F 515 MET cc_start: 0.6906 (OUTLIER) cc_final: 0.6382 (pp-130) REVERT: A 437 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.6672 (mt0) REVERT: A 441 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7415 (tm-30) REVERT: A 443 LYS cc_start: 0.8886 (mmtt) cc_final: 0.8520 (mmmt) REVERT: A 450 GLN cc_start: 0.8576 (tm-30) cc_final: 0.7825 (tm-30) REVERT: A 461 ASP cc_start: 0.8914 (t70) cc_final: 0.8439 (t70) REVERT: A 469 ILE cc_start: 0.9075 (tp) cc_final: 0.8833 (tt) REVERT: A 473 ASP cc_start: 0.8410 (p0) cc_final: 0.8096 (p0) REVERT: A 474 TYR cc_start: 0.7624 (t80) cc_final: 0.7171 (t80) REVERT: A 482 THR cc_start: 0.8168 (t) cc_final: 0.7809 (t) REVERT: A 500 GLU cc_start: 0.6916 (mp0) cc_final: 0.6659 (mp0) REVERT: B 443 LYS cc_start: 0.9078 (mmtt) cc_final: 0.8523 (tptp) REVERT: B 450 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8253 (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: 0.8637 (tt) REVERT: B 482 THR cc_start: 0.8173 (t) cc_final: 0.7811 (t) REVERT: B 500 GLU cc_start: 0.6218 (mp0) cc_final: 0.5933 (mp0) REVERT: B 515 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6892 (pp-130) REVERT: C 440 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.9106 (mt) REVERT: C 450 GLN cc_start: 0.8604 (tm-30) cc_final: 0.7963 (tm-30) REVERT: C 458 GLN cc_start: 0.8599 (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: 0.8386 (t) cc_final: 0.8037 (t) REVERT: C 505 ILE cc_start: 0.8974 (tt) cc_final: 0.8711 (tt) REVERT: D 443 LYS cc_start: 0.8961 (mmtt) cc_final: 0.8237 (mmtt) REVERT: D 450 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8257 (tm-30) REVERT: D 451 MET cc_start: 0.7936 (tpp) cc_final: 0.7679 (tpt) REVERT: D 457 ASN cc_start: 0.9398 (m110) cc_final: 0.9114 (m-40) REVERT: D 460 LEU cc_start: 0.8905 (tt) cc_final: 0.8581 (tt) REVERT: D 469 ILE cc_start: 0.9050 (tp) cc_final: 0.8756 (tt) REVERT: D 473 ASP cc_start: 0.8509 (p0) cc_final: 0.8150 (p0) REVERT: D 474 TYR cc_start: 0.7514 (t80) cc_final: 0.6763 (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: 0.6643 (pp-130) REVERT: E 443 LYS cc_start: 0.8864 (mmtt) cc_final: 0.8576 (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: 0.7842 (pt0) REVERT: E 474 TYR cc_start: 0.7654 (t80) cc_final: 0.7265 (t80) REVERT: E 500 GLU cc_start: 0.7121 (mp0) cc_final: 0.6853 (mp0) REVERT: E 515 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6701 (pp-130) REVERT: G 443 LYS cc_start: 0.8785 (mmtt) cc_final: 0.8539 (tptp) REVERT: G 474 TYR cc_start: 0.7648 (t80) cc_final: 0.7440 (t80) REVERT: H 444 ARG cc_start: 0.8943 (ttt180) cc_final: 0.8743 (ttt180) REVERT: H 515 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6532 (pp-130) REVERT: I 443 LYS cc_start: 0.8813 (mmtt) cc_final: 0.8448 (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: 0.5999 (mp0) REVERT: I 507 GLN cc_start: 0.7874 (pm20) cc_final: 0.7666 (pm20) REVERT: J 439 TRP cc_start: 0.8007 (t60) cc_final: 0.7355 (t60) REVERT: J 441 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7748 (mp10) REVERT: J 443 LYS cc_start: 0.8787 (mmtt) cc_final: 0.8558 (mtpp) REVERT: J 444 ARG cc_start: 0.9038 (ttt180) cc_final: 0.8721 (ttt180) REVERT: J 473 ASP cc_start: 0.8583 (p0) cc_final: 0.8236 (p0) REVERT: J 507 GLN cc_start: 0.7845 (pm20) cc_final: 0.7572 (pm20) REVERT: J 515 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6591 (pp-130) outliers start: 37 outliers final: 11 residues processed: 365 average time/residue: 0.2144 time to fit residues: 99.2506 Evaluate side-chains 354 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 332 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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: 9.9990 chunk 6 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 20.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 = 0.127885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.113494 restraints weight = 13505.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.117129 restraints weight = 7343.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.119724 restraints weight = 4612.922| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6930 Z= 0.214 Angle : 0.811 10.228 9300 Z= 0.382 Chirality : 0.045 0.131 1100 Planarity : 0.002 0.017 1190 Dihedral : 5.889 16.943 900 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 5.57 % Allowed : 17.09 % Favored : 77.34 % 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: -4.69 (0.24), residues: 840 helix: -3.82 (0.13), residues: 570 sheet: None (None), residues: 0 loop : -0.77 (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 I 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 397 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 353 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 443 LYS cc_start: 0.8977 (mmtt) cc_final: 0.8605 (tptp) REVERT: F 444 ARG cc_start: 0.8925 (ttt180) cc_final: 0.8690 (ttt180) REVERT: F 450 GLN cc_start: 0.8335 (tm-30) cc_final: 0.8008 (tm-30) REVERT: F 451 MET cc_start: 0.8307 (tpp) cc_final: 0.8052 (tpp) REVERT: F 474 TYR cc_start: 0.7282 (t80) cc_final: 0.6769 (t80) REVERT: A 437 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.6687 (mt0) REVERT: A 441 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7182 (tm-30) REVERT: A 450 GLN cc_start: 0.8503 (tm-30) cc_final: 0.7775 (tm-30) REVERT: A 458 GLN cc_start: 0.8486 (pt0) cc_final: 0.8110 (pt0) REVERT: A 469 ILE cc_start: 0.8989 (tp) cc_final: 0.8752 (tt) REVERT: A 473 ASP cc_start: 0.8465 (p0) cc_final: 0.8043 (p0) REVERT: A 482 THR cc_start: 0.8084 (t) cc_final: 0.7718 (t) REVERT: B 441 GLN cc_start: 0.7779 (mp10) cc_final: 0.7520 (mp10) REVERT: B 450 GLN cc_start: 0.8422 (tm-30) cc_final: 0.8110 (tm-30) REVERT: B 451 MET cc_start: 0.8064 (tpt) cc_final: 0.7841 (tpt) REVERT: B 469 ILE cc_start: 0.9025 (tp) cc_final: 0.8662 (tt) REVERT: B 482 THR cc_start: 0.8137 (t) cc_final: 0.7768 (t) REVERT: B 515 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.6760 (pp-130) REVERT: B 517 LEU cc_start: 0.7701 (mt) cc_final: 0.7472 (mp) REVERT: C 440 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.9112 (mt) REVERT: C 443 LYS cc_start: 0.8904 (mmtt) cc_final: 0.8444 (mtpp) REVERT: C 450 GLN cc_start: 0.8492 (tm-30) cc_final: 0.7994 (tm-30) REVERT: C 451 MET cc_start: 0.8178 (tpt) cc_final: 0.7923 (tpt) REVERT: C 469 ILE cc_start: 0.8973 (tp) cc_final: 0.8685 (tt) REVERT: C 482 THR cc_start: 0.8321 (t) cc_final: 0.8001 (t) REVERT: C 505 ILE cc_start: 0.8849 (tt) cc_final: 0.8616 (tt) REVERT: D 450 GLN cc_start: 0.8480 (tm-30) cc_final: 0.8066 (tm-30) REVERT: D 461 ASP cc_start: 0.8870 (t70) cc_final: 0.8537 (t0) REVERT: D 469 ILE cc_start: 0.8960 (tp) cc_final: 0.8623 (tt) REVERT: D 473 ASP cc_start: 0.8551 (p0) cc_final: 0.8200 (p0) REVERT: D 474 TYR cc_start: 0.7415 (t80) cc_final: 0.6775 (t80) REVERT: D 507 GLN cc_start: 0.7486 (pm20) cc_final: 0.7213 (pm20) REVERT: D 515 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6273 (pp-130) REVERT: E 450 GLN cc_start: 0.8387 (tm-30) cc_final: 0.7883 (tm-30) REVERT: E 451 MET cc_start: 0.8157 (tpp) cc_final: 0.7923 (tpt) REVERT: E 500 GLU cc_start: 0.7276 (mp0) cc_final: 0.6955 (mp0) REVERT: E 515 MET cc_start: 0.6988 (OUTLIER) cc_final: 0.6405 (pp-130) REVERT: G 441 GLN cc_start: 0.8131 (mp10) cc_final: 0.7701 (mp10) REVERT: G 451 MET cc_start: 0.8114 (tpt) cc_final: 0.7914 (tpt) REVERT: G 458 GLN cc_start: 0.8732 (pt0) cc_final: 0.8319 (pt0) REVERT: H 444 ARG cc_start: 0.9032 (ttt180) cc_final: 0.8691 (ttt180) REVERT: H 450 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8284 (tm-30) REVERT: H 451 MET cc_start: 0.8283 (tpt) cc_final: 0.7826 (tpt) REVERT: H 457 ASN cc_start: 0.8899 (m-40) cc_final: 0.8596 (m-40) REVERT: H 500 GLU cc_start: 0.6613 (mp0) cc_final: 0.6339 (mp0) REVERT: H 515 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.6492 (pp-130) REVERT: I 451 MET cc_start: 0.8543 (tpp) cc_final: 0.8290 (tpt) REVERT: I 457 ASN cc_start: 0.8803 (m-40) cc_final: 0.8525 (m-40) REVERT: I 482 THR cc_start: 0.8243 (t) cc_final: 0.7905 (t) REVERT: I 500 GLU cc_start: 0.6524 (mp0) cc_final: 0.6168 (mp0) REVERT: I 507 GLN cc_start: 0.7898 (pm20) cc_final: 0.7693 (pm20) REVERT: J 441 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8125 (mp10) REVERT: J 443 LYS cc_start: 0.8822 (mmtt) cc_final: 0.8551 (tptp) REVERT: J 444 ARG cc_start: 0.9173 (ttt180) cc_final: 0.8940 (ttt180) REVERT: J 457 ASN cc_start: 0.8823 (m-40) cc_final: 0.8471 (m-40) REVERT: J 470 MET cc_start: 0.7273 (mtp) cc_final: 0.6987 (mtt) REVERT: J 473 ASP cc_start: 0.8544 (p0) cc_final: 0.8136 (p0) REVERT: J 500 GLU cc_start: 0.6125 (mp0) cc_final: 0.5876 (mp0) REVERT: J 507 GLN cc_start: 0.7882 (pm20) cc_final: 0.7678 (pm20) outliers start: 44 outliers final: 25 residues processed: 366 average time/residue: 0.2038 time to fit residues: 95.4588 Evaluate side-chains 370 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 337 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 440 ILE 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: 5.9990 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 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 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.126242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.111183 restraints weight = 13713.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.114896 restraints weight = 7440.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.117541 restraints weight = 4680.751| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6930 Z= 0.242 Angle : 0.854 13.026 9300 Z= 0.391 Chirality : 0.045 0.132 1100 Planarity : 0.003 0.016 1190 Dihedral : 5.829 18.343 900 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 5.70 % Allowed : 19.75 % Favored : 74.56 % 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: -4.83 (0.23), residues: 840 helix: -3.42 (0.15), residues: 590 sheet: None (None), residues: 0 loop : -1.96 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 439 PHE 0.013 0.004 PHE B 501 TYR 0.009 0.001 TYR B 474 ARG 0.003 0.001 ARG B 483 *********************** 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 388 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 343 time to evaluate : 0.828 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: 0.9036 (ttt180) cc_final: 0.8718 (ttt180) REVERT: F 450 GLN cc_start: 0.8462 (tm-30) cc_final: 0.8119 (tm-30) REVERT: F 458 GLN cc_start: 0.8453 (pt0) cc_final: 0.8032 (pt0) REVERT: A 437 GLN cc_start: 0.7962 (mt0) cc_final: 0.6986 (mt0) REVERT: A 441 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7181 (tm-30) REVERT: A 450 GLN cc_start: 0.8549 (tm-30) cc_final: 0.7711 (tm-30) REVERT: A 469 ILE cc_start: 0.9023 (tp) cc_final: 0.8747 (tt) REVERT: A 473 ASP cc_start: 0.8516 (p0) cc_final: 0.8114 (p0) REVERT: A 482 THR cc_start: 0.8217 (t) cc_final: 0.7859 (t) REVERT: B 443 LYS cc_start: 0.8680 (mtpp) cc_final: 0.8314 (mtpp) REVERT: B 450 GLN cc_start: 0.8482 (tm-30) cc_final: 0.7600 (tm-30) REVERT: B 451 MET cc_start: 0.8153 (tpt) cc_final: 0.7633 (tpt) REVERT: B 458 GLN cc_start: 0.8486 (pt0) cc_final: 0.8246 (pt0) REVERT: B 469 ILE cc_start: 0.9108 (tp) cc_final: 0.8747 (tt) REVERT: B 482 THR cc_start: 0.7749 (t) cc_final: 0.7286 (t) REVERT: B 515 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.6949 (pp-130) REVERT: C 443 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8410 (mtpp) REVERT: C 450 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8100 (tm-30) REVERT: C 451 MET cc_start: 0.8031 (tpt) cc_final: 0.7774 (tpt) REVERT: C 458 GLN cc_start: 0.8378 (pt0) cc_final: 0.7807 (pt0) REVERT: C 469 ILE cc_start: 0.8973 (tp) cc_final: 0.8695 (tt) REVERT: C 482 THR cc_start: 0.8359 (t) cc_final: 0.8052 (t) REVERT: C 505 ILE cc_start: 0.8997 (tt) cc_final: 0.8794 (tt) REVERT: D 445 GLU cc_start: 0.8445 (tp30) cc_final: 0.7941 (tp30) REVERT: D 450 GLN cc_start: 0.8561 (tm-30) cc_final: 0.8195 (tm-30) REVERT: D 469 ILE cc_start: 0.9011 (tp) cc_final: 0.8690 (tt) REVERT: D 473 ASP cc_start: 0.8490 (p0) cc_final: 0.8149 (p0) REVERT: D 489 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8670 (mm-40) REVERT: D 515 MET cc_start: 0.6760 (OUTLIER) cc_final: 0.6408 (pp-130) REVERT: E 450 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8098 (tm-30) REVERT: E 451 MET cc_start: 0.8369 (tpp) cc_final: 0.7991 (tpt) REVERT: E 500 GLU cc_start: 0.7252 (mp0) cc_final: 0.6942 (mp0) REVERT: E 515 MET cc_start: 0.6988 (OUTLIER) cc_final: 0.6509 (pp-130) REVERT: G 450 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8119 (tm-30) REVERT: G 451 MET cc_start: 0.8342 (tpt) cc_final: 0.8035 (tpt) REVERT: G 458 GLN cc_start: 0.8730 (pt0) cc_final: 0.8347 (pt0) REVERT: G 500 GLU cc_start: 0.6678 (mp0) cc_final: 0.6468 (mp0) REVERT: H 443 LYS cc_start: 0.8741 (mtpp) cc_final: 0.8069 (mtpp) REVERT: H 444 ARG cc_start: 0.9049 (ttt180) cc_final: 0.8323 (ttt180) REVERT: H 450 GLN cc_start: 0.8787 (tm-30) cc_final: 0.8324 (tm-30) REVERT: H 451 MET cc_start: 0.8285 (tpt) cc_final: 0.7791 (tpt) REVERT: H 457 ASN cc_start: 0.8786 (m-40) cc_final: 0.8235 (t0) REVERT: H 500 GLU cc_start: 0.6743 (mp0) cc_final: 0.6419 (mp0) REVERT: H 515 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.6430 (pp-130) REVERT: H 517 LEU cc_start: 0.7364 (mp) cc_final: 0.6925 (mp) REVERT: I 451 MET cc_start: 0.8591 (tpp) cc_final: 0.8382 (tpt) REVERT: I 457 ASN cc_start: 0.8809 (m-40) cc_final: 0.8515 (m-40) REVERT: I 482 THR cc_start: 0.8406 (t) cc_final: 0.8145 (t) REVERT: I 500 GLU cc_start: 0.6400 (mp0) cc_final: 0.6052 (mp0) REVERT: J 441 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8083 (mp10) REVERT: J 443 LYS cc_start: 0.8699 (mmtt) cc_final: 0.8434 (mtpp) REVERT: J 444 ARG cc_start: 0.9126 (ttt180) cc_final: 0.8855 (ttt180) REVERT: J 450 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8040 (tm-30) REVERT: J 457 ASN cc_start: 0.8738 (m-40) cc_final: 0.8472 (m-40) REVERT: J 473 ASP cc_start: 0.8544 (p0) cc_final: 0.8086 (p0) REVERT: J 500 GLU cc_start: 0.6294 (mp0) cc_final: 0.6021 (mp0) REVERT: J 507 GLN cc_start: 0.7959 (pm20) cc_final: 0.7716 (pm20) outliers start: 45 outliers final: 29 residues processed: 355 average time/residue: 0.1971 time to fit residues: 89.8046 Evaluate side-chains 370 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 334 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 504 VAL 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 504 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain D residue 489 GLN 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 482 THR 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 509 LEU Chi-restraints excluded: chain H residue 453 GLU Chi-restraints excluded: chain H residue 470 MET 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: 7.9990 chunk 10 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 512 ASN ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 512 ASN G 457 ASN I 489 GLN I 512 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.132817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.118376 restraints weight = 13111.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.122166 restraints weight = 7072.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.124675 restraints weight = 4396.519| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6930 Z= 0.166 Angle : 0.820 11.568 9300 Z= 0.364 Chirality : 0.043 0.136 1100 Planarity : 0.003 0.023 1190 Dihedral : 5.419 18.348 900 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 6.96 % Allowed : 19.49 % Favored : 73.54 % 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: -3.96 (0.26), residues: 840 helix: -2.89 (0.17), residues: 590 sheet: None (None), residues: 0 loop : -1.29 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 439 PHE 0.009 0.003 PHE F 501 TYR 0.008 0.001 TYR I 474 ARG 0.007 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 418 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 363 time to evaluate : 0.795 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 450 GLN cc_start: 0.8631 (tm-30) cc_final: 0.8280 (tm-30) REVERT: F 451 MET cc_start: 0.8180 (tpt) cc_final: 0.7690 (tpt) REVERT: F 458 GLN cc_start: 0.8293 (pt0) cc_final: 0.7726 (pt0) REVERT: F 515 MET cc_start: 0.6396 (pp-130) cc_final: 0.5975 (pp-130) REVERT: A 437 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.6892 (mt0) REVERT: A 441 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7265 (tm-30) REVERT: A 443 LYS cc_start: 0.8764 (mtpt) cc_final: 0.8412 (mtpp) REVERT: A 450 GLN cc_start: 0.8483 (tm-30) cc_final: 0.7665 (tm-30) REVERT: A 458 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7243 (pt0) REVERT: A 469 ILE cc_start: 0.8866 (tp) cc_final: 0.8624 (tt) REVERT: A 473 ASP cc_start: 0.8471 (p0) cc_final: 0.7987 (p0) REVERT: A 482 THR cc_start: 0.8013 (t) cc_final: 0.7683 (t) REVERT: A 500 GLU cc_start: 0.6025 (mp0) cc_final: 0.5823 (mp0) REVERT: B 450 GLN cc_start: 0.8497 (tm-30) cc_final: 0.7623 (tm-30) REVERT: B 451 MET cc_start: 0.8138 (tpt) cc_final: 0.7604 (tpt) REVERT: B 461 ASP cc_start: 0.8912 (t70) cc_final: 0.8671 (t0) REVERT: B 469 ILE cc_start: 0.8963 (tp) cc_final: 0.8632 (tt) REVERT: B 482 THR cc_start: 0.8296 (t) cc_final: 0.7960 (t) REVERT: C 443 LYS cc_start: 0.8892 (mmtt) cc_final: 0.8434 (mmmt) REVERT: C 450 GLN cc_start: 0.8581 (tm-30) cc_final: 0.8006 (tm-30) REVERT: C 451 MET cc_start: 0.8109 (tpt) cc_final: 0.7902 (tpt) REVERT: C 458 GLN cc_start: 0.8203 (pt0) cc_final: 0.7349 (pt0) REVERT: C 461 ASP cc_start: 0.8880 (t70) cc_final: 0.8616 (t0) REVERT: C 469 ILE cc_start: 0.8802 (tp) cc_final: 0.8587 (tt) REVERT: C 505 ILE cc_start: 0.8757 (tt) cc_final: 0.8552 (tt) REVERT: D 450 GLN cc_start: 0.8449 (tm-30) cc_final: 0.7476 (tm-30) REVERT: D 461 ASP cc_start: 0.8670 (t70) cc_final: 0.8379 (t0) REVERT: D 469 ILE cc_start: 0.8869 (tp) cc_final: 0.8549 (tt) REVERT: D 473 ASP cc_start: 0.8388 (p0) cc_final: 0.8076 (p0) REVERT: D 515 MET cc_start: 0.6724 (OUTLIER) cc_final: 0.6035 (pp-130) REVERT: D 517 LEU cc_start: 0.7375 (mp) cc_final: 0.6747 (mp) REVERT: E 443 LYS cc_start: 0.8494 (mtpp) cc_final: 0.8162 (mtpp) REVERT: E 450 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8105 (tm-30) REVERT: E 451 MET cc_start: 0.8471 (tpp) cc_final: 0.8008 (tpt) REVERT: E 461 ASP cc_start: 0.8851 (t70) cc_final: 0.8353 (t70) REVERT: E 472 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.5648 (pp20) REVERT: E 500 GLU cc_start: 0.7147 (mp0) cc_final: 0.6872 (mp0) REVERT: E 515 MET cc_start: 0.6776 (OUTLIER) cc_final: 0.6434 (pp-130) REVERT: G 450 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8212 (tm-30) REVERT: G 451 MET cc_start: 0.8368 (tpt) cc_final: 0.8130 (tpt) REVERT: G 458 GLN cc_start: 0.8651 (pt0) cc_final: 0.8357 (pt0) REVERT: H 443 LYS cc_start: 0.8419 (mtpp) cc_final: 0.8129 (mtpp) REVERT: H 450 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8015 (tm-30) REVERT: H 451 MET cc_start: 0.8226 (tpt) cc_final: 0.7790 (tpt) REVERT: H 457 ASN cc_start: 0.8773 (m-40) cc_final: 0.8298 (t0) REVERT: H 458 GLN cc_start: 0.8815 (pt0) cc_final: 0.8291 (pt0) REVERT: H 482 THR cc_start: 0.8533 (t) cc_final: 0.8227 (t) REVERT: H 500 GLU cc_start: 0.6554 (mp0) cc_final: 0.6272 (mp0) REVERT: H 515 MET cc_start: 0.6906 (OUTLIER) cc_final: 0.6298 (pp-130) REVERT: I 451 MET cc_start: 0.8552 (tpp) cc_final: 0.8326 (tpt) REVERT: I 457 ASN cc_start: 0.8684 (m-40) cc_final: 0.8288 (t0) REVERT: I 482 THR cc_start: 0.8383 (t) cc_final: 0.8056 (t) REVERT: I 500 GLU cc_start: 0.6794 (mp0) cc_final: 0.6314 (mp0) REVERT: J 441 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8036 (mp10) REVERT: J 443 LYS cc_start: 0.8751 (mmtt) cc_final: 0.8440 (mtpp) REVERT: J 444 ARG cc_start: 0.9067 (ttt180) cc_final: 0.8849 (ttt180) REVERT: J 451 MET cc_start: 0.8327 (tpt) cc_final: 0.7940 (tpt) REVERT: J 453 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8156 (pp20) REVERT: J 457 ASN cc_start: 0.8595 (m-40) cc_final: 0.8133 (t0) REVERT: J 470 MET cc_start: 0.7283 (mtp) cc_final: 0.5758 (mtp) REVERT: J 473 ASP cc_start: 0.8492 (p0) cc_final: 0.8067 (p0) REVERT: J 500 GLU cc_start: 0.6264 (mp0) cc_final: 0.5962 (mp0) outliers start: 55 outliers final: 32 residues processed: 377 average time/residue: 0.2261 time to fit residues: 107.8465 Evaluate side-chains 377 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 336 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 448 VAL 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 448 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 491 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 458 GLN 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 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 491 LEU Chi-restraints excluded: chain H residue 515 MET Chi-restraints excluded: chain I residue 460 LEU Chi-restraints excluded: chain I residue 491 LEU 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 504 VAL Chi-restraints excluded: chain J residue 509 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 68 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 ASN ** 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** ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 ASN B 514 GLN ** C 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** G 457 ASN ** H 441 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 = 0.3595 r_free = 0.3595 target = 0.130219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.115955 restraints weight = 13500.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.119632 restraints weight = 7293.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.122269 restraints weight = 4534.321| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.5276 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= 0.213 Angle : 0.840 11.168 9300 Z= 0.381 Chirality : 0.044 0.138 1100 Planarity : 0.003 0.019 1190 Dihedral : 5.461 14.941 900 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 5.70 % Allowed : 21.77 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.46 (0.27), residues: 840 helix: -2.67 (0.18), residues: 570 sheet: None (None), residues: 0 loop : -0.85 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 439 PHE 0.013 0.004 PHE C 501 TYR 0.007 0.001 TYR I 474 ARG 0.005 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 391 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 346 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 445 GLU cc_start: 0.8263 (tp30) cc_final: 0.7891 (tp30) REVERT: F 450 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8235 (tm-30) REVERT: F 451 MET cc_start: 0.8244 (tpt) cc_final: 0.7722 (tpt) REVERT: F 458 GLN cc_start: 0.8395 (pt0) cc_final: 0.8032 (pt0) REVERT: F 482 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8156 (t) REVERT: F 500 GLU cc_start: 0.6424 (mp0) cc_final: 0.6143 (mm-30) REVERT: F 515 MET cc_start: 0.6640 (pp-130) cc_final: 0.5973 (pp-130) REVERT: A 437 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.6992 (mt0) REVERT: A 441 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7412 (tm-30) REVERT: A 443 LYS cc_start: 0.8772 (mtpt) cc_final: 0.8381 (mtpp) REVERT: A 450 GLN cc_start: 0.8533 (tm-30) cc_final: 0.7557 (tm-30) REVERT: A 458 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7005 (pt0) REVERT: A 469 ILE cc_start: 0.8923 (tp) cc_final: 0.8628 (tt) REVERT: A 473 ASP cc_start: 0.8501 (p0) cc_final: 0.8214 (p0) REVERT: A 482 THR cc_start: 0.8172 (t) cc_final: 0.7844 (t) REVERT: B 437 GLN cc_start: 0.7226 (mt0) cc_final: 0.6759 (mt0) REVERT: B 450 GLN cc_start: 0.8347 (tm-30) cc_final: 0.7843 (tm-30) REVERT: B 451 MET cc_start: 0.8180 (tpt) cc_final: 0.7707 (tpt) REVERT: B 469 ILE cc_start: 0.9003 (tp) cc_final: 0.8661 (tt) REVERT: B 482 THR cc_start: 0.7795 (t) cc_final: 0.7410 (t) REVERT: C 443 LYS cc_start: 0.8795 (mmtt) cc_final: 0.8379 (mtpp) REVERT: C 450 GLN cc_start: 0.8709 (tm-30) cc_final: 0.8120 (tm-30) REVERT: C 458 GLN cc_start: 0.8248 (pt0) cc_final: 0.7791 (pt0) REVERT: C 469 ILE cc_start: 0.8866 (tp) cc_final: 0.8620 (tt) REVERT: C 482 THR cc_start: 0.8241 (t) cc_final: 0.7956 (t) REVERT: D 437 GLN cc_start: 0.6781 (mm-40) cc_final: 0.6460 (mm-40) REVERT: D 445 GLU cc_start: 0.8505 (tp30) cc_final: 0.7939 (tp30) REVERT: D 450 GLN cc_start: 0.8487 (tm-30) cc_final: 0.8197 (tm-30) REVERT: D 461 ASP cc_start: 0.8775 (t70) cc_final: 0.8177 (t0) REVERT: D 473 ASP cc_start: 0.8441 (p0) cc_final: 0.8135 (p0) REVERT: E 450 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8168 (tm-30) REVERT: E 458 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7913 (pt0) REVERT: E 470 MET cc_start: 0.7529 (mtp) cc_final: 0.6655 (mtp) REVERT: E 472 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.6104 (pp20) REVERT: E 500 GLU cc_start: 0.7098 (mp0) cc_final: 0.6830 (mp0) REVERT: E 515 MET cc_start: 0.6896 (OUTLIER) cc_final: 0.6392 (pp-130) REVERT: G 444 ARG cc_start: 0.8593 (ttt180) cc_final: 0.8084 (ttt180) REVERT: G 450 GLN cc_start: 0.8698 (tm-30) cc_final: 0.7964 (tm-30) REVERT: G 451 MET cc_start: 0.8346 (tpt) cc_final: 0.8052 (tpt) REVERT: G 458 GLN cc_start: 0.8727 (pt0) cc_final: 0.8445 (pt0) REVERT: H 450 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8119 (tm-30) REVERT: H 451 MET cc_start: 0.8238 (tpt) cc_final: 0.7630 (tpt) REVERT: H 457 ASN cc_start: 0.8816 (m-40) cc_final: 0.8123 (t0) REVERT: H 458 GLN cc_start: 0.8900 (pt0) cc_final: 0.8323 (pt0) REVERT: H 466 ARG cc_start: 0.7925 (mtm-85) cc_final: 0.7458 (mtm-85) REVERT: H 482 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8327 (t) REVERT: H 500 GLU cc_start: 0.6589 (mp0) cc_final: 0.6260 (mp0) REVERT: H 515 MET cc_start: 0.6978 (OUTLIER) cc_final: 0.6250 (pp-130) REVERT: H 517 LEU cc_start: 0.7018 (mp) cc_final: 0.6763 (mp) REVERT: I 451 MET cc_start: 0.8550 (tpp) cc_final: 0.8304 (tpt) REVERT: I 457 ASN cc_start: 0.8673 (m-40) cc_final: 0.8332 (t0) REVERT: I 500 GLU cc_start: 0.6858 (mp0) cc_final: 0.6369 (mp0) REVERT: J 441 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8085 (mp10) REVERT: J 443 LYS cc_start: 0.8693 (mmtt) cc_final: 0.8398 (mtpp) REVERT: J 444 ARG cc_start: 0.9086 (ttt180) cc_final: 0.8842 (ttt180) REVERT: J 451 MET cc_start: 0.8342 (tpt) cc_final: 0.7947 (tpt) REVERT: J 457 ASN cc_start: 0.8696 (m-40) cc_final: 0.8321 (t0) REVERT: J 473 ASP cc_start: 0.8369 (p0) cc_final: 0.7888 (p0) REVERT: J 500 GLU cc_start: 0.6202 (mp0) cc_final: 0.5903 (mp0) outliers start: 45 outliers final: 28 residues processed: 356 average time/residue: 0.2223 time to fit residues: 101.4284 Evaluate side-chains 378 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 340 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 437 GLN 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 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 57 optimal weight: 5.9990 chunk 73 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 457 ASN ** 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** D 489 GLN ** 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 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 457 ASN ** H 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 438 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.129239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.114894 restraints weight = 13453.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.118496 restraints weight = 7417.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.121082 restraints weight = 4674.112| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.5415 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= 0.229 Angle : 0.883 11.716 9300 Z= 0.400 Chirality : 0.046 0.175 1100 Planarity : 0.003 0.030 1190 Dihedral : 5.444 16.138 900 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 6.20 % Allowed : 22.15 % Favored : 71.65 % 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: -3.42 (0.27), residues: 840 helix: -2.72 (0.19), residues: 510 sheet: None (None), residues: 0 loop : -1.16 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 439 PHE 0.014 0.004 PHE B 501 TYR 0.008 0.001 TYR I 474 ARG 0.011 0.001 ARG E 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 401 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 352 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 445 GLU cc_start: 0.8174 (tp30) cc_final: 0.7887 (tp30) REVERT: F 450 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8377 (tm-30) REVERT: F 458 GLN cc_start: 0.8362 (pt0) cc_final: 0.7568 (pt0) REVERT: F 515 MET cc_start: 0.6833 (pp-130) cc_final: 0.5927 (pp-130) REVERT: A 437 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.6798 (mt0) REVERT: A 441 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7374 (tm-30) REVERT: A 443 LYS cc_start: 0.8837 (mtpt) cc_final: 0.8506 (mtpp) REVERT: A 450 GLN cc_start: 0.8661 (tm-30) cc_final: 0.7698 (tm-30) REVERT: A 458 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.6867 (pt0) REVERT: A 469 ILE cc_start: 0.8922 (tp) cc_final: 0.8598 (tt) REVERT: A 473 ASP cc_start: 0.8491 (p0) cc_final: 0.8122 (p0) REVERT: A 482 THR cc_start: 0.8264 (t) cc_final: 0.7932 (t) REVERT: A 501 PHE cc_start: 0.8819 (t80) cc_final: 0.8414 (t80) REVERT: B 450 GLN cc_start: 0.8406 (tm-30) cc_final: 0.8179 (tm-30) REVERT: B 469 ILE cc_start: 0.9038 (tp) cc_final: 0.8714 (tt) REVERT: B 482 THR cc_start: 0.7812 (t) cc_final: 0.7429 (t) REVERT: B 500 GLU cc_start: 0.6810 (mp0) cc_final: 0.6562 (mp0) REVERT: C 443 LYS cc_start: 0.8872 (mmtt) cc_final: 0.8449 (mtpp) REVERT: C 450 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8130 (tm-30) REVERT: C 458 GLN cc_start: 0.8281 (pt0) cc_final: 0.7460 (pt0) REVERT: C 469 ILE cc_start: 0.8911 (tp) cc_final: 0.8681 (tt) REVERT: C 482 THR cc_start: 0.8269 (OUTLIER) cc_final: 0.7971 (t) REVERT: C 488 ARG cc_start: 0.8475 (mtm180) cc_final: 0.8099 (mtm180) REVERT: C 500 GLU cc_start: 0.6594 (mp0) cc_final: 0.6352 (mp0) REVERT: D 437 GLN cc_start: 0.6770 (mm-40) cc_final: 0.6466 (mm-40) REVERT: D 445 GLU cc_start: 0.8441 (tp30) cc_final: 0.7965 (tp30) REVERT: D 450 GLN cc_start: 0.8484 (tm-30) cc_final: 0.7521 (tm-30) REVERT: E 443 LYS cc_start: 0.8437 (mtpp) cc_final: 0.8040 (ptpt) REVERT: E 450 GLN cc_start: 0.8800 (tm-30) cc_final: 0.8093 (tm-30) REVERT: E 458 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.7992 (pt0) REVERT: E 470 MET cc_start: 0.7533 (mtp) cc_final: 0.6572 (mtp) REVERT: E 472 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.6133 (pp20) REVERT: E 500 GLU cc_start: 0.7148 (mp0) cc_final: 0.6920 (mp0) REVERT: E 515 MET cc_start: 0.6832 (OUTLIER) cc_final: 0.6395 (pp-130) REVERT: G 441 GLN cc_start: 0.7957 (mp10) cc_final: 0.7641 (mp10) REVERT: G 450 GLN cc_start: 0.8693 (tm-30) cc_final: 0.7942 (tm-30) REVERT: G 451 MET cc_start: 0.8401 (tpt) cc_final: 0.8040 (tpt) REVERT: G 458 GLN cc_start: 0.8755 (pt0) cc_final: 0.8455 (pt0) REVERT: H 450 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8388 (tm-30) REVERT: H 451 MET cc_start: 0.8404 (tpt) cc_final: 0.7619 (tpt) REVERT: H 457 ASN cc_start: 0.8826 (m-40) cc_final: 0.8075 (t0) REVERT: H 458 GLN cc_start: 0.8893 (pt0) cc_final: 0.8408 (pt0) REVERT: H 482 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8356 (t) REVERT: H 500 GLU cc_start: 0.6723 (mp0) cc_final: 0.6317 (mp0) REVERT: H 515 MET cc_start: 0.7089 (OUTLIER) cc_final: 0.6515 (pp-130) REVERT: H 517 LEU cc_start: 0.7111 (mp) cc_final: 0.6847 (mp) REVERT: I 450 GLN cc_start: 0.8613 (tm-30) cc_final: 0.7692 (tm-30) REVERT: I 451 MET cc_start: 0.8528 (tpp) cc_final: 0.7350 (ttm) REVERT: I 457 ASN cc_start: 0.8770 (m-40) cc_final: 0.8316 (t0) REVERT: I 482 THR cc_start: 0.8514 (OUTLIER) cc_final: 0.8241 (t) REVERT: I 500 GLU cc_start: 0.6840 (mp0) cc_final: 0.6324 (mp0) REVERT: J 441 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8132 (mp10) REVERT: J 443 LYS cc_start: 0.8741 (mmtt) cc_final: 0.8434 (mtpp) REVERT: J 444 ARG cc_start: 0.9081 (ttt180) cc_final: 0.8830 (ttt180) REVERT: J 451 MET cc_start: 0.8207 (tpt) cc_final: 0.7572 (ttt) REVERT: J 457 ASN cc_start: 0.8693 (m-40) cc_final: 0.8266 (t0) REVERT: J 470 MET cc_start: 0.7435 (mtp) cc_final: 0.5441 (mtp) REVERT: J 473 ASP cc_start: 0.8395 (p0) cc_final: 0.7999 (p0) REVERT: J 500 GLU cc_start: 0.6359 (mp0) cc_final: 0.6074 (mp0) outliers start: 49 outliers final: 35 residues processed: 362 average time/residue: 0.1999 time to fit residues: 92.6447 Evaluate side-chains 394 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 348 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 437 GLN 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 458 GLN 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 447 ILE Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 460 LEU 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 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 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 H residue 515 MET 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 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 509 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 27 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 57 optimal weight: 20.0000 chunk 77 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 chunk 25 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 68 optimal weight: 0.2980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 438 GLN 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** ** D 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 438 GLN ** E 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 457 ASN H 438 GLN ** H 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.133289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.118792 restraints weight = 13309.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.122525 restraints weight = 7263.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.125025 restraints weight = 4542.141| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.5686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6930 Z= 0.195 Angle : 0.887 12.101 9300 Z= 0.398 Chirality : 0.045 0.163 1100 Planarity : 0.003 0.025 1190 Dihedral : 5.229 20.481 900 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 6.58 % Allowed : 22.91 % Favored : 70.51 % 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: -3.64 (0.26), residues: 840 helix: -2.43 (0.20), residues: 550 sheet: None (None), residues: 0 loop : -2.00 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 439 PHE 0.012 0.003 PHE F 501 TYR 0.008 0.001 TYR I 474 ARG 0.007 0.001 ARG B 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 401 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 349 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 445 GLU cc_start: 0.8180 (tp30) cc_final: 0.7882 (pm20) REVERT: F 450 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8325 (tm-30) REVERT: F 458 GLN cc_start: 0.8352 (pt0) cc_final: 0.7513 (pt0) REVERT: F 500 GLU cc_start: 0.6433 (mp0) cc_final: 0.6107 (mm-30) REVERT: F 515 MET cc_start: 0.6719 (pp-130) cc_final: 0.5962 (pp-130) REVERT: A 437 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.6986 (mt0) REVERT: A 441 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7273 (tm-30) REVERT: A 443 LYS cc_start: 0.8784 (mtpt) cc_final: 0.8479 (mtpp) REVERT: A 450 GLN cc_start: 0.8673 (tm-30) cc_final: 0.7717 (tm-30) REVERT: A 458 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.6987 (pt0) REVERT: A 469 ILE cc_start: 0.8911 (tp) cc_final: 0.8640 (tt) REVERT: A 473 ASP cc_start: 0.8485 (p0) cc_final: 0.8079 (p0) REVERT: A 482 THR cc_start: 0.8233 (t) cc_final: 0.7916 (t) REVERT: A 501 PHE cc_start: 0.8769 (t80) cc_final: 0.8465 (t80) REVERT: B 441 GLN cc_start: 0.7806 (mp10) cc_final: 0.6866 (tp40) REVERT: B 461 ASP cc_start: 0.8895 (t0) cc_final: 0.8664 (t0) REVERT: B 466 ARG cc_start: 0.8398 (mtm-85) cc_final: 0.8162 (mpp80) REVERT: B 469 ILE cc_start: 0.8959 (tp) cc_final: 0.8670 (tt) REVERT: B 482 THR cc_start: 0.8225 (t) cc_final: 0.7855 (t) REVERT: B 500 GLU cc_start: 0.6732 (mp0) cc_final: 0.6505 (mp0) REVERT: C 443 LYS cc_start: 0.8797 (mmtt) cc_final: 0.8379 (mtpp) REVERT: C 450 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8153 (tm-30) REVERT: C 469 ILE cc_start: 0.8879 (tp) cc_final: 0.8652 (tt) REVERT: C 488 ARG cc_start: 0.8454 (mtm180) cc_final: 0.8004 (mtm180) REVERT: C 500 GLU cc_start: 0.6621 (mp0) cc_final: 0.6385 (mp0) REVERT: D 437 GLN cc_start: 0.6635 (mm-40) cc_final: 0.6258 (mm-40) REVERT: D 445 GLU cc_start: 0.8394 (tp30) cc_final: 0.8155 (tp30) REVERT: D 450 GLN cc_start: 0.8538 (tm-30) cc_final: 0.8169 (tm-30) REVERT: D 461 ASP cc_start: 0.8748 (t0) cc_final: 0.8198 (t0) REVERT: D 501 PHE cc_start: 0.8587 (t80) cc_final: 0.8356 (t80) REVERT: E 443 LYS cc_start: 0.8349 (mtpp) cc_final: 0.8002 (ptpt) REVERT: E 445 GLU cc_start: 0.8334 (tp30) cc_final: 0.8051 (tp30) REVERT: E 450 GLN cc_start: 0.8731 (tm-30) cc_final: 0.8123 (tm-30) REVERT: E 451 MET cc_start: 0.8034 (tpt) cc_final: 0.7400 (tpt) REVERT: E 458 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8054 (pt0) REVERT: E 470 MET cc_start: 0.7422 (mtp) cc_final: 0.6443 (mtp) REVERT: E 472 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.6048 (pp20) REVERT: E 515 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.6120 (pp-130) REVERT: E 518 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7759 (tm-30) REVERT: G 441 GLN cc_start: 0.7856 (mp10) cc_final: 0.7551 (mp10) REVERT: G 444 ARG cc_start: 0.8590 (ttt180) cc_final: 0.8132 (ttt180) REVERT: G 450 GLN cc_start: 0.8711 (tm-30) cc_final: 0.7929 (tm-30) REVERT: G 451 MET cc_start: 0.8363 (tpt) cc_final: 0.8053 (tpt) REVERT: G 458 GLN cc_start: 0.8697 (pt0) cc_final: 0.8349 (pt0) REVERT: G 515 MET cc_start: 0.6649 (pp-130) cc_final: 0.5824 (pp-130) REVERT: H 450 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8361 (tm-30) REVERT: H 451 MET cc_start: 0.8336 (tpt) cc_final: 0.7603 (tpt) REVERT: H 457 ASN cc_start: 0.8859 (m-40) cc_final: 0.8386 (t0) REVERT: H 458 GLN cc_start: 0.8879 (pt0) cc_final: 0.8412 (pt0) REVERT: H 482 THR cc_start: 0.8538 (t) cc_final: 0.8310 (t) REVERT: H 500 GLU cc_start: 0.6731 (mp0) cc_final: 0.6350 (mp0) REVERT: H 515 MET cc_start: 0.6947 (OUTLIER) cc_final: 0.6429 (pp-130) REVERT: H 517 LEU cc_start: 0.7182 (mp) cc_final: 0.6834 (mp) REVERT: I 450 GLN cc_start: 0.8636 (tm-30) cc_final: 0.7650 (tm-30) REVERT: I 451 MET cc_start: 0.8553 (tpp) cc_final: 0.7306 (ttm) REVERT: I 457 ASN cc_start: 0.8750 (m-40) cc_final: 0.8311 (t0) REVERT: I 482 THR cc_start: 0.8483 (t) cc_final: 0.8220 (t) REVERT: I 500 GLU cc_start: 0.6976 (mp0) cc_final: 0.6504 (mp0) REVERT: I 515 MET cc_start: 0.6456 (pp-130) cc_final: 0.5678 (pp-130) REVERT: J 441 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8094 (mp10) REVERT: J 443 LYS cc_start: 0.8667 (mmtt) cc_final: 0.8389 (mtpp) REVERT: J 444 ARG cc_start: 0.8918 (ttt180) cc_final: 0.8467 (ttt180) REVERT: J 451 MET cc_start: 0.8198 (tpt) cc_final: 0.7507 (ttt) REVERT: J 457 ASN cc_start: 0.8633 (m-40) cc_final: 0.8270 (t0) REVERT: J 470 MET cc_start: 0.7395 (mtp) cc_final: 0.5547 (mtp) REVERT: J 500 GLU cc_start: 0.6235 (mp0) cc_final: 0.5948 (mp0) outliers start: 52 outliers final: 36 residues processed: 361 average time/residue: 0.2280 time to fit residues: 103.5130 Evaluate side-chains 378 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 334 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 437 GLN 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 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 448 VAL Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 460 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 447 ILE 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 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 491 LEU Chi-restraints excluded: chain H residue 509 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 28 optimal weight: 0.0970 chunk 26 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 457 ASN ** D 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.132749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.118189 restraints weight = 13385.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.121956 restraints weight = 7313.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.124622 restraints weight = 4563.437| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.5800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6930 Z= 0.220 Angle : 0.937 11.838 9300 Z= 0.425 Chirality : 0.046 0.172 1100 Planarity : 0.003 0.044 1190 Dihedral : 5.268 19.972 900 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 5.70 % Allowed : 25.06 % 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: -3.10 (0.28), residues: 840 helix: -2.30 (0.20), residues: 570 sheet: None (None), residues: 0 loop : -0.97 (0.42), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 439 PHE 0.013 0.003 PHE A 501 TYR 0.008 0.001 TYR I 474 ARG 0.008 0.001 ARG F 466 *********************** 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 378 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 333 time to evaluate : 2.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 450 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8327 (tm-30) REVERT: F 451 MET cc_start: 0.8168 (tpt) cc_final: 0.7829 (tpt) REVERT: F 453 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8265 (tm-30) REVERT: F 458 GLN cc_start: 0.8479 (pt0) cc_final: 0.7690 (pt0) REVERT: F 515 MET cc_start: 0.6802 (pp-130) cc_final: 0.5907 (pp-130) REVERT: A 437 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7045 (mt0) REVERT: A 441 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7292 (tm-30) REVERT: A 443 LYS cc_start: 0.8800 (mtpt) cc_final: 0.8479 (mtpp) REVERT: A 450 GLN cc_start: 0.8759 (tm-30) cc_final: 0.7749 (tm-30) REVERT: A 451 MET cc_start: 0.8061 (tpt) cc_final: 0.7694 (tpt) REVERT: A 458 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7003 (pt0) REVERT: A 469 ILE cc_start: 0.8920 (tp) cc_final: 0.8655 (tt) REVERT: A 473 ASP cc_start: 0.8498 (p0) cc_final: 0.8195 (p0) REVERT: A 482 THR cc_start: 0.8249 (t) cc_final: 0.7914 (t) REVERT: A 501 PHE cc_start: 0.8744 (t80) cc_final: 0.8447 (t80) REVERT: B 441 GLN cc_start: 0.7857 (mp10) cc_final: 0.7521 (tp40) REVERT: B 466 ARG cc_start: 0.8460 (mtm-85) cc_final: 0.8222 (mpp80) REVERT: B 469 ILE cc_start: 0.8984 (tp) cc_final: 0.8699 (tt) REVERT: B 482 THR cc_start: 0.8208 (t) cc_final: 0.7840 (t) REVERT: B 500 GLU cc_start: 0.6736 (mp0) cc_final: 0.6490 (mp0) REVERT: C 443 LYS cc_start: 0.8793 (mmtt) cc_final: 0.8387 (mtpp) REVERT: C 450 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8187 (tm-30) REVERT: C 469 ILE cc_start: 0.8914 (tp) cc_final: 0.8682 (tt) REVERT: C 500 GLU cc_start: 0.6651 (mp0) cc_final: 0.6398 (mp0) REVERT: D 437 GLN cc_start: 0.6546 (mm-40) cc_final: 0.6297 (mm-40) REVERT: D 445 GLU cc_start: 0.8366 (tp30) cc_final: 0.8122 (tp30) REVERT: D 450 GLN cc_start: 0.8529 (tm-30) cc_final: 0.8221 (tm-30) REVERT: E 443 LYS cc_start: 0.8348 (mtpp) cc_final: 0.7981 (ptpt) REVERT: E 445 GLU cc_start: 0.8314 (tp30) cc_final: 0.8050 (tp30) REVERT: E 450 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8089 (tm-30) REVERT: E 457 ASN cc_start: 0.9048 (m-40) cc_final: 0.8781 (m110) REVERT: E 458 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8120 (pt0) REVERT: E 470 MET cc_start: 0.7512 (mtp) cc_final: 0.6475 (mtp) REVERT: E 472 GLU cc_start: 0.6677 (OUTLIER) cc_final: 0.6089 (pp20) REVERT: E 515 MET cc_start: 0.6349 (OUTLIER) cc_final: 0.5725 (pp-130) REVERT: G 450 GLN cc_start: 0.8727 (tm-30) cc_final: 0.7934 (tm-30) REVERT: G 451 MET cc_start: 0.8320 (tpt) cc_final: 0.7987 (tpt) REVERT: G 458 GLN cc_start: 0.8675 (pt0) cc_final: 0.8311 (pt0) REVERT: G 515 MET cc_start: 0.6757 (pp-130) cc_final: 0.6015 (pp-130) REVERT: H 450 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8374 (tm-30) REVERT: H 451 MET cc_start: 0.8390 (tpt) cc_final: 0.7676 (tpt) REVERT: H 457 ASN cc_start: 0.8836 (m-40) cc_final: 0.8333 (t0) REVERT: H 458 GLN cc_start: 0.8897 (pt0) cc_final: 0.8434 (pt0) REVERT: H 482 THR cc_start: 0.8563 (t) cc_final: 0.8316 (t) REVERT: H 500 GLU cc_start: 0.6727 (mp0) cc_final: 0.6377 (mp0) REVERT: H 515 MET cc_start: 0.7077 (OUTLIER) cc_final: 0.6504 (pp-130) REVERT: I 450 GLN cc_start: 0.8626 (tm-30) cc_final: 0.7637 (tm-30) REVERT: I 451 MET cc_start: 0.8549 (tpp) cc_final: 0.7342 (ttm) REVERT: I 457 ASN cc_start: 0.8759 (m-40) cc_final: 0.8309 (t0) REVERT: I 482 THR cc_start: 0.8470 (OUTLIER) cc_final: 0.8195 (t) REVERT: I 488 ARG cc_start: 0.8740 (mtm-85) cc_final: 0.8527 (mtm180) REVERT: I 500 GLU cc_start: 0.6890 (mp0) cc_final: 0.6416 (mp0) REVERT: I 515 MET cc_start: 0.6545 (pp-130) cc_final: 0.5785 (pp-130) REVERT: J 441 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8154 (mp10) REVERT: J 443 LYS cc_start: 0.8690 (mmtt) cc_final: 0.8396 (mtpp) REVERT: J 444 ARG cc_start: 0.9003 (ttt180) cc_final: 0.8650 (ttt180) REVERT: J 451 MET cc_start: 0.8089 (tpt) cc_final: 0.7555 (ttt) REVERT: J 457 ASN cc_start: 0.8674 (m-40) cc_final: 0.8324 (t0) REVERT: J 470 MET cc_start: 0.7471 (mtp) cc_final: 0.5657 (mtp) REVERT: J 500 GLU cc_start: 0.6241 (mp0) cc_final: 0.5970 (mp0) outliers start: 45 outliers final: 35 residues processed: 341 average time/residue: 0.2212 time to fit residues: 96.3994 Evaluate side-chains 369 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 324 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 453 GLU Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain A residue 437 GLN 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 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 448 VAL Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 460 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 447 ILE 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 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 509 LEU Chi-restraints excluded: chain H residue 515 MET 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 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 495 ASP 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: 9.9990 chunk 25 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 11 optimal weight: 0.0670 chunk 48 optimal weight: 4.9990 chunk 47 optimal weight: 30.0000 overall best weight: 5.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** 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 437 GLN ** E 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 = 0.3579 r_free = 0.3579 target = 0.129946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.115382 restraints weight = 13744.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.119081 restraints weight = 7520.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.121675 restraints weight = 4706.317| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.5829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6930 Z= 0.280 Angle : 0.987 12.318 9300 Z= 0.451 Chirality : 0.048 0.178 1100 Planarity : 0.004 0.052 1190 Dihedral : 5.468 20.048 900 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.44 % Allowed : 26.20 % Favored : 68.35 % 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: -3.13 (0.28), residues: 840 helix: -2.29 (0.20), residues: 570 sheet: None (None), residues: 0 loop : -1.06 (0.42), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 439 PHE 0.018 0.004 PHE B 501 TYR 0.008 0.002 TYR F 474 ARG 0.008 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 383 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 340 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: F 450 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8314 (tm-30) REVERT: F 451 MET cc_start: 0.8339 (tpt) cc_final: 0.7878 (tpt) REVERT: F 458 GLN cc_start: 0.8447 (pt0) cc_final: 0.7580 (pt0) REVERT: F 515 MET cc_start: 0.7043 (pp-130) cc_final: 0.5974 (pp-130) REVERT: A 437 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.6898 (mt0) REVERT: A 441 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7342 (tm-30) REVERT: A 443 LYS cc_start: 0.8855 (mtpt) cc_final: 0.8518 (mtpp) REVERT: A 450 GLN cc_start: 0.8799 (tm-30) cc_final: 0.7895 (tm-30) REVERT: A 458 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.6898 (pt0) REVERT: A 469 ILE cc_start: 0.8951 (tp) cc_final: 0.8663 (tt) REVERT: A 473 ASP cc_start: 0.8482 (p0) cc_final: 0.8155 (p0) REVERT: A 482 THR cc_start: 0.8342 (t) cc_final: 0.8026 (t) REVERT: A 501 PHE cc_start: 0.8871 (t80) cc_final: 0.8624 (t80) REVERT: B 441 GLN cc_start: 0.7828 (mp10) cc_final: 0.7435 (tp40) REVERT: B 458 GLN cc_start: 0.8535 (pt0) cc_final: 0.8289 (pt0) REVERT: B 469 ILE cc_start: 0.8998 (tp) cc_final: 0.8714 (tt) REVERT: B 482 THR cc_start: 0.7829 (t) cc_final: 0.7439 (t) REVERT: B 500 GLU cc_start: 0.6815 (mp0) cc_final: 0.6522 (mp0) REVERT: C 443 LYS cc_start: 0.8847 (mmtt) cc_final: 0.8468 (mtpp) REVERT: C 450 GLN cc_start: 0.8898 (tm-30) cc_final: 0.8050 (tm-30) REVERT: C 469 ILE cc_start: 0.8984 (tp) cc_final: 0.8721 (tt) REVERT: C 488 ARG cc_start: 0.8525 (mtm180) cc_final: 0.8164 (mtm180) REVERT: D 445 GLU cc_start: 0.8426 (tp30) cc_final: 0.7997 (tp30) REVERT: D 450 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8036 (tm-30) REVERT: E 445 GLU cc_start: 0.8368 (tp30) cc_final: 0.8153 (tp30) REVERT: E 450 GLN cc_start: 0.8672 (tm-30) cc_final: 0.7989 (tm-30) REVERT: E 451 MET cc_start: 0.8173 (tpt) cc_final: 0.7598 (tpt) REVERT: E 457 ASN cc_start: 0.9023 (m-40) cc_final: 0.8732 (m110) REVERT: E 458 GLN cc_start: 0.8495 (pt0) cc_final: 0.8218 (pt0) REVERT: E 470 MET cc_start: 0.7530 (mtp) cc_final: 0.6432 (mtp) REVERT: E 472 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6185 (pp20) REVERT: E 515 MET cc_start: 0.6476 (OUTLIER) cc_final: 0.6046 (pp-130) REVERT: G 437 GLN cc_start: 0.7505 (mt0) cc_final: 0.7297 (mt0) REVERT: G 450 GLN cc_start: 0.8671 (tm-30) cc_final: 0.7944 (tm-30) REVERT: G 451 MET cc_start: 0.8381 (tpt) cc_final: 0.7986 (tpt) REVERT: G 458 GLN cc_start: 0.8679 (pt0) cc_final: 0.8328 (pt0) REVERT: H 450 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8340 (tm-30) REVERT: H 451 MET cc_start: 0.8463 (tpt) cc_final: 0.7789 (tpt) REVERT: H 457 ASN cc_start: 0.8929 (m-40) cc_final: 0.8168 (t0) REVERT: H 458 GLN cc_start: 0.9036 (pt0) cc_final: 0.8535 (pt0) REVERT: H 482 THR cc_start: 0.8599 (t) cc_final: 0.8361 (t) REVERT: H 500 GLU cc_start: 0.6779 (mp0) cc_final: 0.6436 (mp0) REVERT: I 450 GLN cc_start: 0.8663 (tm-30) cc_final: 0.7725 (tm-30) REVERT: I 451 MET cc_start: 0.8567 (tpp) cc_final: 0.7388 (ttm) REVERT: I 457 ASN cc_start: 0.8850 (m-40) cc_final: 0.8384 (t0) REVERT: I 500 GLU cc_start: 0.6747 (mp0) cc_final: 0.6244 (mp0) REVERT: I 515 MET cc_start: 0.6724 (pp-130) cc_final: 0.6098 (pp-130) REVERT: J 441 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8192 (mp10) REVERT: J 443 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8418 (mtpp) REVERT: J 444 ARG cc_start: 0.9097 (ttt180) cc_final: 0.8758 (ttt180) REVERT: J 450 GLN cc_start: 0.8764 (tm-30) cc_final: 0.7934 (tm-30) REVERT: J 451 MET cc_start: 0.8161 (tpt) cc_final: 0.7365 (ttm) REVERT: J 457 ASN cc_start: 0.8689 (m-40) cc_final: 0.8301 (t0) REVERT: J 470 MET cc_start: 0.7584 (mtp) cc_final: 0.5681 (mtp) REVERT: J 500 GLU cc_start: 0.6146 (mp0) cc_final: 0.5863 (mp0) outliers start: 43 outliers final: 34 residues processed: 349 average time/residue: 0.1921 time to fit residues: 86.7136 Evaluate side-chains 373 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 333 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 453 GLU Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain A residue 437 GLN 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 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 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 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 453 GLU 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 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 495 ASP 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 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 495 ASP 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: 8.9990 chunk 77 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 ASN A 514 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 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 438 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.129810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.115410 restraints weight = 13562.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.119035 restraints weight = 7459.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.121555 restraints weight = 4693.751| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.5950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6930 Z= 0.264 Angle : 0.992 11.843 9300 Z= 0.453 Chirality : 0.048 0.173 1100 Planarity : 0.003 0.052 1190 Dihedral : 5.522 20.177 900 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 5.32 % Allowed : 26.46 % Favored : 68.23 % 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: -3.23 (0.27), residues: 840 helix: -2.43 (0.20), residues: 510 sheet: None (None), residues: 0 loop : -1.34 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 439 PHE 0.023 0.004 PHE D 501 TYR 0.008 0.002 TYR I 474 ARG 0.008 0.001 ARG B 466 =============================================================================== Job complete usr+sys time: 2384.71 seconds wall clock time: 42 minutes 16.68 seconds (2536.68 seconds total)