Starting phenix.real_space_refine on Tue Sep 24 03:09:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ggs_4399/09_2024/6ggs_4399.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ggs_4399/09_2024/6ggs_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ggs_4399/09_2024/6ggs_4399.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ggs_4399/09_2024/6ggs_4399.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ggs_4399/09_2024/6ggs_4399.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ggs_4399/09_2024/6ggs_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-5461/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: 2.57, per 1000 atoms: 0.37 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: 1.77 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.73 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: 1.65 Time building geometry restraints manager: 2.10 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' 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: 0.080 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.180 Find NCS groups from input model: 0.250 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.780 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 10 poor density : 399 time to evaluate : 0.799 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: 0.2031 time to fit residues: 104.8367 Evaluate side-chains 335 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 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 fitting. rotamer outliers: 37 poor density : 362 time to evaluate : 0.911 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: 0.8111 (t60) cc_final: 0.7393 (t60) REVERT: F 443 LYS cc_start: 0.8883 (mmtt) cc_final: 0.8606 (mtpp) REVERT: F 444 ARG cc_start: 0.8898 (ttt180) cc_final: 0.8564 (ttt180) REVERT: F 450 GLN cc_start: 0.8403 (tm-30) cc_final: 0.8175 (tm-30) REVERT: F 451 MET cc_start: 0.8306 (tpp) cc_final: 0.8062 (tpt) REVERT: F 457 ASN cc_start: 0.9341 (m110) cc_final: 0.8902 (m-40) REVERT: F 460 LEU cc_start: 0.8966 (tt) cc_final: 0.8725 (tt) REVERT: F 474 TYR cc_start: 0.7483 (t80) cc_final: 0.6689 (t80) REVERT: F 515 MET cc_start: 0.6984 (OUTLIER) cc_final: 0.6383 (pp-130) REVERT: A 437 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.6640 (mt0) REVERT: A 441 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7508 (tm-30) REVERT: A 443 LYS cc_start: 0.8909 (mmtt) cc_final: 0.8501 (mmmt) REVERT: A 450 GLN cc_start: 0.8564 (tm-30) cc_final: 0.7776 (tm-30) REVERT: A 457 ASN cc_start: 0.9193 (m110) cc_final: 0.8988 (m-40) REVERT: A 461 ASP cc_start: 0.8947 (t70) cc_final: 0.8518 (t70) REVERT: A 469 ILE cc_start: 0.9045 (tp) cc_final: 0.8805 (tt) REVERT: A 473 ASP cc_start: 0.8354 (p0) cc_final: 0.8083 (p0) REVERT: A 474 TYR cc_start: 0.7590 (t80) cc_final: 0.7100 (t80) REVERT: A 482 THR cc_start: 0.8100 (t) cc_final: 0.7741 (t) REVERT: A 500 GLU cc_start: 0.6840 (mp0) cc_final: 0.6584 (mp0) REVERT: A 507 GLN cc_start: 0.7757 (pm20) cc_final: 0.7539 (pm20) REVERT: A 515 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6907 (pp-130) REVERT: B 443 LYS cc_start: 0.9082 (mmtt) cc_final: 0.8506 (tptp) REVERT: B 450 GLN cc_start: 0.8614 (tm-30) cc_final: 0.8207 (tm-30) REVERT: B 457 ASN cc_start: 0.9203 (m110) cc_final: 0.8907 (m-40) REVERT: B 469 ILE cc_start: 0.8992 (tp) cc_final: 0.8607 (tt) REVERT: B 482 THR cc_start: 0.8134 (t) cc_final: 0.7776 (t) REVERT: B 500 GLU cc_start: 0.6160 (mp0) cc_final: 0.5873 (mp0) REVERT: B 515 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.6880 (pp-130) REVERT: C 450 GLN cc_start: 0.8555 (tm-30) cc_final: 0.7907 (tm-30) REVERT: C 458 GLN cc_start: 0.8588 (pt0) cc_final: 0.7962 (pt0) REVERT: C 469 ILE cc_start: 0.9005 (tp) cc_final: 0.8680 (tt) REVERT: C 482 THR cc_start: 0.8330 (t) cc_final: 0.7983 (t) REVERT: C 505 ILE cc_start: 0.8874 (tt) cc_final: 0.8598 (tt) REVERT: D 443 LYS cc_start: 0.8999 (mmtt) cc_final: 0.8226 (mmtt) REVERT: D 450 GLN cc_start: 0.8588 (tm-30) cc_final: 0.8219 (tm-30) REVERT: D 451 MET cc_start: 0.7917 (tpp) cc_final: 0.7658 (tpt) REVERT: D 457 ASN cc_start: 0.9408 (m110) cc_final: 0.9127 (m-40) REVERT: D 460 LEU cc_start: 0.8993 (tt) cc_final: 0.8642 (tt) REVERT: D 469 ILE cc_start: 0.9031 (tp) cc_final: 0.8722 (tt) REVERT: D 473 ASP cc_start: 0.8504 (p0) cc_final: 0.8221 (p0) REVERT: D 474 TYR cc_start: 0.7454 (t80) cc_final: 0.6635 (t80) REVERT: D 489 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8504 (mm-40) REVERT: D 515 MET cc_start: 0.7120 (OUTLIER) cc_final: 0.6608 (pp-130) REVERT: E 443 LYS cc_start: 0.8878 (mmtt) cc_final: 0.8559 (mmmt) REVERT: E 450 GLN cc_start: 0.8402 (tm-30) cc_final: 0.7937 (tm-30) REVERT: E 451 MET cc_start: 0.8114 (tpp) cc_final: 0.7878 (tpt) REVERT: E 458 GLN cc_start: 0.8298 (pt0) cc_final: 0.7779 (pt0) REVERT: E 474 TYR cc_start: 0.7680 (t80) cc_final: 0.7231 (t80) REVERT: E 500 GLU cc_start: 0.7116 (mp0) cc_final: 0.6833 (mp0) REVERT: E 515 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.6680 (pp-130) REVERT: G 443 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8525 (tptp) REVERT: G 474 TYR cc_start: 0.7733 (t80) cc_final: 0.7464 (t80) REVERT: H 444 ARG cc_start: 0.8890 (ttt180) cc_final: 0.8667 (ttt180) REVERT: H 515 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.6538 (pp-130) REVERT: I 443 LYS cc_start: 0.8868 (mmtt) cc_final: 0.8430 (tptp) REVERT: I 450 GLN cc_start: 0.8719 (tm-30) cc_final: 0.7995 (tm-30) REVERT: I 451 MET cc_start: 0.8441 (tpp) cc_final: 0.8044 (tpt) REVERT: I 482 THR cc_start: 0.8220 (t) cc_final: 0.7859 (t) REVERT: I 500 GLU cc_start: 0.6246 (mp0) cc_final: 0.5925 (mp0) REVERT: I 507 GLN cc_start: 0.7857 (pm20) cc_final: 0.7640 (pm20) REVERT: I 515 MET cc_start: 0.6770 (OUTLIER) cc_final: 0.6495 (pp-130) REVERT: J 439 TRP cc_start: 0.8051 (t60) cc_final: 0.7368 (t60) REVERT: J 441 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.7854 (mp10) REVERT: J 443 LYS cc_start: 0.8817 (mmtt) cc_final: 0.8492 (mtpp) REVERT: J 444 ARG cc_start: 0.8961 (ttt180) cc_final: 0.8638 (ttt180) REVERT: J 473 ASP cc_start: 0.8610 (p0) cc_final: 0.8320 (p0) REVERT: J 507 GLN cc_start: 0.7828 (pm20) cc_final: 0.7542 (pm20) REVERT: J 515 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6580 (pp-130) outliers start: 37 outliers final: 11 residues processed: 365 average time/residue: 0.2155 time to fit residues: 99.3843 Evaluate side-chains 354 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 331 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 A residue 515 MET 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 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 I 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 40 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 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 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6930 Z= 0.270 Angle : 0.834 10.114 9300 Z= 0.397 Chirality : 0.046 0.137 1100 Planarity : 0.003 0.016 1190 Dihedral : 6.021 17.197 900 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 6.20 % Allowed : 16.71 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.73 (0.24), residues: 840 helix: -3.85 (0.13), residues: 570 sheet: None (None), residues: 0 loop : -0.80 (0.42), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 439 PHE 0.012 0.004 PHE F 501 TYR 0.009 0.001 TYR B 474 ARG 0.003 0.001 ARG B 483 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 349 time to evaluate : 0.774 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: F 439 TRP cc_start: 0.8110 (t60) cc_final: 0.7409 (t60) REVERT: F 443 LYS cc_start: 0.8976 (mmtt) cc_final: 0.8623 (mtpp) REVERT: F 444 ARG cc_start: 0.8902 (ttt180) cc_final: 0.8660 (ttt180) REVERT: F 450 GLN cc_start: 0.8333 (tm-30) cc_final: 0.8003 (tm-30) REVERT: F 451 MET cc_start: 0.8341 (tpp) cc_final: 0.8100 (tpp) REVERT: F 460 LEU cc_start: 0.8917 (tt) cc_final: 0.8678 (tt) REVERT: F 474 TYR cc_start: 0.7463 (t80) cc_final: 0.6974 (t80) REVERT: A 437 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.6646 (mt0) REVERT: A 441 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7167 (tm-30) REVERT: A 450 GLN cc_start: 0.8546 (tm-30) cc_final: 0.7710 (tm-30) REVERT: A 469 ILE cc_start: 0.9027 (tp) cc_final: 0.8777 (tt) REVERT: A 473 ASP cc_start: 0.8410 (p0) cc_final: 0.8128 (p0) REVERT: A 482 THR cc_start: 0.8131 (t) cc_final: 0.7769 (t) REVERT: A 500 GLU cc_start: 0.7007 (mp0) cc_final: 0.6802 (mp0) REVERT: A 507 GLN cc_start: 0.7992 (pm20) cc_final: 0.7735 (pm20) REVERT: A 515 MET cc_start: 0.7157 (OUTLIER) cc_final: 0.6692 (pp-130) REVERT: B 437 GLN cc_start: 0.7672 (mt0) cc_final: 0.7310 (mt0) REVERT: B 441 GLN cc_start: 0.7906 (mp10) cc_final: 0.7158 (mp10) REVERT: B 443 LYS cc_start: 0.8922 (mmtt) cc_final: 0.8670 (mtpp) REVERT: B 450 GLN cc_start: 0.8423 (tm-30) cc_final: 0.8054 (tm-30) REVERT: B 451 MET cc_start: 0.8053 (tpt) cc_final: 0.7814 (tpt) REVERT: B 469 ILE cc_start: 0.9062 (tp) cc_final: 0.8700 (tt) REVERT: B 482 THR cc_start: 0.7836 (t) cc_final: 0.7487 (t) REVERT: B 515 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.6787 (pp-130) REVERT: B 517 LEU cc_start: 0.7674 (mt) cc_final: 0.7437 (mp) REVERT: C 443 LYS cc_start: 0.9040 (mmtt) cc_final: 0.8426 (mtpp) REVERT: C 450 GLN cc_start: 0.8485 (tm-30) cc_final: 0.7984 (tm-30) REVERT: C 451 MET cc_start: 0.8138 (tpt) cc_final: 0.7894 (tpt) REVERT: C 469 ILE cc_start: 0.8960 (tp) cc_final: 0.8663 (tt) REVERT: C 482 THR cc_start: 0.8322 (t) cc_final: 0.8050 (t) REVERT: C 505 ILE cc_start: 0.8857 (tt) cc_final: 0.8631 (tt) REVERT: D 443 LYS cc_start: 0.8845 (mmtt) cc_final: 0.8609 (mtpp) REVERT: D 450 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8094 (tm-30) REVERT: D 458 GLN cc_start: 0.8545 (pt0) cc_final: 0.8012 (pt0) REVERT: D 460 LEU cc_start: 0.9035 (tt) cc_final: 0.8723 (tt) REVERT: D 461 ASP cc_start: 0.9028 (t70) cc_final: 0.8681 (t70) REVERT: D 469 ILE cc_start: 0.9004 (tp) cc_final: 0.8630 (tt) REVERT: D 473 ASP cc_start: 0.8582 (p0) cc_final: 0.8317 (p0) REVERT: D 474 TYR cc_start: 0.7579 (t80) cc_final: 0.6794 (t80) REVERT: D 507 GLN cc_start: 0.7512 (pm20) cc_final: 0.7252 (pm20) REVERT: D 515 MET cc_start: 0.7024 (OUTLIER) cc_final: 0.6385 (pp-130) REVERT: D 517 LEU cc_start: 0.7606 (mt) cc_final: 0.7347 (mp) REVERT: E 443 LYS cc_start: 0.8796 (mmtt) cc_final: 0.8586 (mmmt) REVERT: E 450 GLN cc_start: 0.8472 (tm-30) cc_final: 0.8022 (tm-30) REVERT: E 451 MET cc_start: 0.8186 (tpp) cc_final: 0.7911 (tpt) REVERT: E 482 THR cc_start: 0.8347 (t) cc_final: 0.7930 (t) REVERT: E 500 GLU cc_start: 0.7119 (mp0) cc_final: 0.6822 (mp0) REVERT: E 515 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6440 (pp-130) REVERT: G 441 GLN cc_start: 0.8420 (mp10) cc_final: 0.8143 (mp10) REVERT: G 443 LYS cc_start: 0.8864 (mmtt) cc_final: 0.8595 (mtpp) REVERT: G 450 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8316 (tm-30) REVERT: G 451 MET cc_start: 0.8207 (tpt) cc_final: 0.7968 (tpt) REVERT: G 458 GLN cc_start: 0.8740 (pt0) cc_final: 0.8346 (pt0) REVERT: H 439 TRP cc_start: 0.8398 (t60) cc_final: 0.8150 (t60) REVERT: H 444 ARG cc_start: 0.8965 (ttt180) cc_final: 0.8631 (ttt180) REVERT: H 450 GLN cc_start: 0.8945 (tm-30) cc_final: 0.8434 (tm-30) REVERT: H 451 MET cc_start: 0.8178 (tpt) cc_final: 0.7715 (tpt) REVERT: H 457 ASN cc_start: 0.8945 (m-40) cc_final: 0.8630 (m-40) REVERT: H 500 GLU cc_start: 0.6616 (mp0) cc_final: 0.6319 (mp0) REVERT: H 515 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.6536 (pp-130) REVERT: I 443 LYS cc_start: 0.8818 (mmtt) cc_final: 0.8578 (mtpp) REVERT: I 450 GLN cc_start: 0.8741 (tm-30) cc_final: 0.7988 (tm-30) REVERT: I 451 MET cc_start: 0.8677 (tpp) cc_final: 0.8227 (tpt) REVERT: I 457 ASN cc_start: 0.8804 (m-40) cc_final: 0.8561 (m-40) REVERT: I 469 ILE cc_start: 0.9036 (tp) cc_final: 0.8801 (tt) REVERT: I 482 THR cc_start: 0.8249 (t) cc_final: 0.7993 (t) REVERT: I 500 GLU cc_start: 0.6593 (mp0) cc_final: 0.6239 (mp0) REVERT: I 507 GLN cc_start: 0.7928 (pm20) cc_final: 0.7682 (pm20) REVERT: I 515 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.6528 (pp-130) REVERT: J 439 TRP cc_start: 0.8025 (t60) cc_final: 0.7578 (t60) REVERT: J 441 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8201 (mp10) REVERT: J 443 LYS cc_start: 0.8869 (mmtt) cc_final: 0.8421 (mtpp) REVERT: J 444 ARG cc_start: 0.9138 (ttt180) cc_final: 0.8903 (ttt180) REVERT: J 450 GLN cc_start: 0.8748 (tm-30) cc_final: 0.7877 (tm-30) REVERT: J 457 ASN cc_start: 0.8876 (m-40) cc_final: 0.8520 (m-40) REVERT: J 466 ARG cc_start: 0.8377 (mpp-170) cc_final: 0.8100 (mtm-85) REVERT: J 470 MET cc_start: 0.7595 (mtp) cc_final: 0.7241 (mtt) REVERT: J 473 ASP cc_start: 0.8615 (p0) cc_final: 0.8316 (p0) REVERT: J 507 GLN cc_start: 0.7951 (pm20) cc_final: 0.7691 (pm20) REVERT: J 515 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.7108 (pp-130) outliers start: 49 outliers final: 31 residues processed: 362 average time/residue: 0.2068 time to fit residues: 95.5131 Evaluate side-chains 385 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 344 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 504 VAL 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 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 A residue 515 MET Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain E residue 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 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 515 MET Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 509 LEU Chi-restraints excluded: chain J residue 515 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 77 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 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** ** F 514 GLN ** 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 457 ASN 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6930 Z= 0.241 Angle : 0.827 11.102 9300 Z= 0.382 Chirality : 0.045 0.154 1100 Planarity : 0.003 0.016 1190 Dihedral : 5.675 16.384 900 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 7.22 % Allowed : 17.47 % Favored : 75.32 % 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: -4.77 (0.23), residues: 840 helix: -3.37 (0.15), residues: 590 sheet: None (None), residues: 0 loop : -1.98 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 439 PHE 0.013 0.004 PHE F 501 TYR 0.008 0.002 TYR B 474 ARG 0.006 0.001 ARG H 466 *********************** 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 405 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 348 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 439 TRP cc_start: 0.8232 (t60) cc_final: 0.7829 (t60) REVERT: F 441 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8647 (pm20) REVERT: F 443 LYS cc_start: 0.9038 (mmtt) cc_final: 0.8578 (mtpp) REVERT: F 444 ARG cc_start: 0.9006 (ttt180) cc_final: 0.8713 (ttt180) REVERT: F 450 GLN cc_start: 0.8434 (tm-30) cc_final: 0.8060 (tm-30) REVERT: F 458 GLN cc_start: 0.8523 (pt0) cc_final: 0.8108 (pt0) REVERT: F 460 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8714 (tt) REVERT: F 474 TYR cc_start: 0.7457 (t80) cc_final: 0.7106 (t80) REVERT: F 500 GLU cc_start: 0.6439 (mp0) cc_final: 0.6228 (mp0) REVERT: A 437 GLN cc_start: 0.8052 (mt0) cc_final: 0.6914 (mt0) REVERT: A 441 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7323 (tm-30) REVERT: A 450 GLN cc_start: 0.8625 (tm-30) cc_final: 0.7703 (tm-30) REVERT: A 451 MET cc_start: 0.8292 (tpt) cc_final: 0.7895 (tpt) REVERT: A 458 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7257 (pt0) REVERT: A 469 ILE cc_start: 0.8989 (tp) cc_final: 0.8725 (tt) REVERT: A 473 ASP cc_start: 0.8500 (p0) cc_final: 0.8228 (p0) REVERT: A 482 THR cc_start: 0.8101 (t) cc_final: 0.7731 (t) REVERT: A 507 GLN cc_start: 0.7968 (pm20) cc_final: 0.7664 (pm20) REVERT: A 515 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6599 (pp-130) REVERT: B 443 LYS cc_start: 0.9052 (mmtt) cc_final: 0.8714 (mtpp) REVERT: B 450 GLN cc_start: 0.8444 (tm-30) cc_final: 0.7533 (tm-30) REVERT: B 451 MET cc_start: 0.8129 (tpt) cc_final: 0.7596 (tpt) REVERT: B 458 GLN cc_start: 0.8503 (pt0) cc_final: 0.8219 (pt0) REVERT: B 469 ILE cc_start: 0.9090 (tp) cc_final: 0.8738 (tt) REVERT: B 482 THR cc_start: 0.7748 (t) cc_final: 0.7312 (t) REVERT: B 515 MET cc_start: 0.7432 (OUTLIER) cc_final: 0.7016 (pp-130) REVERT: B 517 LEU cc_start: 0.7750 (mt) cc_final: 0.7495 (mp) REVERT: C 443 LYS cc_start: 0.9026 (mmtt) cc_final: 0.8414 (mtpp) REVERT: C 450 GLN cc_start: 0.8561 (tm-30) cc_final: 0.7977 (tm-30) REVERT: C 451 MET cc_start: 0.8063 (tpt) cc_final: 0.7805 (tpt) REVERT: C 458 GLN cc_start: 0.8376 (pt0) cc_final: 0.7659 (pt0) REVERT: C 469 ILE cc_start: 0.8955 (tp) cc_final: 0.8673 (tt) REVERT: C 482 THR cc_start: 0.8312 (t) cc_final: 0.8072 (t) REVERT: D 443 LYS cc_start: 0.8983 (mmtt) cc_final: 0.8664 (mtpp) REVERT: D 450 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8095 (tm-30) REVERT: D 457 ASN cc_start: 0.9258 (m-40) cc_final: 0.9020 (m-40) REVERT: D 460 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8760 (tt) REVERT: D 461 ASP cc_start: 0.9084 (t70) cc_final: 0.8679 (t0) REVERT: D 469 ILE cc_start: 0.8967 (tp) cc_final: 0.8650 (tt) REVERT: D 473 ASP cc_start: 0.8480 (p0) cc_final: 0.8250 (p0) REVERT: D 474 TYR cc_start: 0.7628 (t80) cc_final: 0.6767 (t80) REVERT: D 515 MET cc_start: 0.7122 (OUTLIER) cc_final: 0.6601 (pp-130) REVERT: D 517 LEU cc_start: 0.7618 (mt) cc_final: 0.7404 (mp) REVERT: E 450 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8099 (tm-30) REVERT: E 451 MET cc_start: 0.8364 (tpp) cc_final: 0.7913 (tpt) REVERT: E 458 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7152 (pt0) REVERT: E 500 GLU cc_start: 0.7277 (mp0) cc_final: 0.6968 (mp0) REVERT: E 515 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6576 (pp-130) REVERT: G 443 LYS cc_start: 0.8882 (mmtt) cc_final: 0.8524 (mtpp) REVERT: G 450 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8195 (tm-30) REVERT: G 451 MET cc_start: 0.8393 (tpt) cc_final: 0.8089 (tpt) REVERT: G 458 GLN cc_start: 0.8685 (pt0) cc_final: 0.8300 (pt0) REVERT: G 500 GLU cc_start: 0.6663 (mp0) cc_final: 0.6458 (mp0) REVERT: H 443 LYS cc_start: 0.8803 (mtpp) cc_final: 0.8100 (mtpp) REVERT: H 444 ARG cc_start: 0.9000 (ttt180) cc_final: 0.8271 (ttt180) REVERT: H 450 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8405 (tm-30) REVERT: H 451 MET cc_start: 0.8266 (tpt) cc_final: 0.7761 (tpt) REVERT: H 457 ASN cc_start: 0.8835 (m-40) cc_final: 0.8340 (t0) REVERT: H 500 GLU cc_start: 0.6657 (mp0) cc_final: 0.6331 (mp0) REVERT: H 515 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6615 (pp-130) REVERT: I 443 LYS cc_start: 0.8848 (mmtt) cc_final: 0.8541 (mtpp) REVERT: I 450 GLN cc_start: 0.8681 (tm-30) cc_final: 0.7843 (tm-30) REVERT: I 451 MET cc_start: 0.8614 (tpp) cc_final: 0.8225 (tpt) REVERT: I 457 ASN cc_start: 0.8804 (m-40) cc_final: 0.8436 (m-40) REVERT: I 469 ILE cc_start: 0.8866 (tp) cc_final: 0.8644 (tt) REVERT: I 482 THR cc_start: 0.8338 (t) cc_final: 0.8063 (t) REVERT: I 500 GLU cc_start: 0.6316 (mp0) cc_final: 0.6001 (mp0) REVERT: I 515 MET cc_start: 0.7024 (OUTLIER) cc_final: 0.6586 (pp-130) REVERT: J 439 TRP cc_start: 0.8142 (t60) cc_final: 0.7712 (t60) REVERT: J 441 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8210 (mp10) REVERT: J 443 LYS cc_start: 0.8812 (mmtt) cc_final: 0.8406 (mtpp) REVERT: J 444 ARG cc_start: 0.9155 (ttt180) cc_final: 0.8900 (ttt180) REVERT: J 450 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8032 (tm-30) REVERT: J 457 ASN cc_start: 0.8723 (m-40) cc_final: 0.8468 (m-40) REVERT: J 466 ARG cc_start: 0.8408 (mpp-170) cc_final: 0.8189 (mtm-85) REVERT: J 470 MET cc_start: 0.7415 (mtp) cc_final: 0.7145 (mtp) REVERT: J 473 ASP cc_start: 0.8591 (p0) cc_final: 0.8225 (p0) REVERT: J 500 GLU cc_start: 0.6223 (mp0) cc_final: 0.5984 (mp0) REVERT: J 507 GLN cc_start: 0.7874 (pm20) cc_final: 0.7623 (pm20) outliers start: 57 outliers final: 32 residues processed: 364 average time/residue: 0.2029 time to fit residues: 94.3388 Evaluate side-chains 382 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 337 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 509 LEU Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 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 A residue 515 MET Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 515 MET 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 460 LEU Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 482 THR Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 515 MET Chi-restraints excluded: chain G residue 460 LEU 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 482 THR Chi-restraints excluded: chain H residue 491 LEU Chi-restraints excluded: chain H residue 504 VAL Chi-restraints excluded: chain H residue 515 MET Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain I residue 504 VAL Chi-restraints excluded: chain I residue 515 MET 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 43 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 53 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 overall best weight: 5.4188 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 GLN ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 GLN ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 GLN E 489 GLN ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 457 ASN ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6930 Z= 0.257 Angle : 0.845 11.762 9300 Z= 0.390 Chirality : 0.045 0.167 1100 Planarity : 0.003 0.016 1190 Dihedral : 5.646 15.435 900 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 7.47 % Allowed : 18.61 % Favored : 73.92 % 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: -4.30 (0.24), residues: 840 helix: -3.00 (0.17), residues: 590 sheet: None (None), residues: 0 loop : -1.83 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 439 PHE 0.018 0.004 PHE H 501 TYR 0.006 0.002 TYR B 474 ARG 0.006 0.001 ARG H 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 416 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 357 time to evaluate : 0.862 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 439 TRP cc_start: 0.8303 (t60) cc_final: 0.7992 (t60) REVERT: F 441 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8408 (pm20) REVERT: F 443 LYS cc_start: 0.9039 (mmtt) cc_final: 0.8531 (mtpp) REVERT: F 444 ARG cc_start: 0.9011 (ttt180) cc_final: 0.8749 (ttt180) REVERT: F 450 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8101 (tm-30) REVERT: F 457 ASN cc_start: 0.9265 (m-40) cc_final: 0.8993 (m-40) REVERT: F 458 GLN cc_start: 0.8494 (pt0) cc_final: 0.8209 (pt0) REVERT: F 460 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8795 (tt) REVERT: F 469 ILE cc_start: 0.8952 (tp) cc_final: 0.8575 (tt) REVERT: F 474 TYR cc_start: 0.7643 (t80) cc_final: 0.7251 (t80) REVERT: F 500 GLU cc_start: 0.6487 (mp0) cc_final: 0.6223 (mp0) REVERT: A 437 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.6910 (mt0) REVERT: A 441 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7389 (tm-30) REVERT: A 443 LYS cc_start: 0.8941 (mtpt) cc_final: 0.8497 (mtpp) REVERT: A 450 GLN cc_start: 0.8619 (tm-30) cc_final: 0.7644 (tm-30) REVERT: A 451 MET cc_start: 0.8306 (tpt) cc_final: 0.7813 (tpt) REVERT: A 458 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7484 (pt0) REVERT: A 469 ILE cc_start: 0.8981 (tp) cc_final: 0.8710 (tt) REVERT: A 473 ASP cc_start: 0.8461 (p0) cc_final: 0.8174 (p0) REVERT: A 482 THR cc_start: 0.8235 (t) cc_final: 0.7864 (t) REVERT: A 500 GLU cc_start: 0.6394 (mp0) cc_final: 0.6165 (mp0) REVERT: A 515 MET cc_start: 0.6909 (OUTLIER) cc_final: 0.6480 (pp-130) REVERT: B 443 LYS cc_start: 0.9065 (mmtt) cc_final: 0.8658 (mtpp) REVERT: B 450 GLN cc_start: 0.8533 (tm-30) cc_final: 0.7644 (tm-30) REVERT: B 451 MET cc_start: 0.8147 (tpt) cc_final: 0.7602 (tpt) REVERT: B 469 ILE cc_start: 0.9123 (tp) cc_final: 0.8810 (tt) REVERT: B 479 THR cc_start: 0.9119 (t) cc_final: 0.8895 (t) REVERT: B 482 THR cc_start: 0.7879 (t) cc_final: 0.7499 (t) REVERT: B 515 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.6733 (pp-130) REVERT: C 443 LYS cc_start: 0.9014 (mmtt) cc_final: 0.8485 (mtpp) REVERT: C 450 GLN cc_start: 0.8612 (tm-30) cc_final: 0.8051 (tm-30) REVERT: C 451 MET cc_start: 0.8035 (tpt) cc_final: 0.7754 (tpt) REVERT: C 458 GLN cc_start: 0.8211 (pt0) cc_final: 0.7330 (pt0) REVERT: C 469 ILE cc_start: 0.8940 (tp) cc_final: 0.8634 (tt) REVERT: C 482 THR cc_start: 0.8211 (t) cc_final: 0.7950 (t) REVERT: C 501 PHE cc_start: 0.8930 (t80) cc_final: 0.8709 (t80) REVERT: D 443 LYS cc_start: 0.8979 (mmtt) cc_final: 0.8652 (mtpp) REVERT: D 445 GLU cc_start: 0.8311 (tp30) cc_final: 0.7846 (tp30) REVERT: D 450 GLN cc_start: 0.8434 (tm-30) cc_final: 0.8065 (tm-30) REVERT: D 457 ASN cc_start: 0.9247 (m-40) cc_final: 0.9010 (m-40) REVERT: D 460 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8836 (tt) REVERT: D 461 ASP cc_start: 0.9101 (t70) cc_final: 0.8801 (t70) REVERT: D 473 ASP cc_start: 0.8502 (p0) cc_final: 0.8294 (p0) REVERT: D 474 TYR cc_start: 0.7787 (t80) cc_final: 0.6894 (t80) REVERT: D 515 MET cc_start: 0.7056 (OUTLIER) cc_final: 0.6751 (pp-130) REVERT: D 517 LEU cc_start: 0.7737 (mt) cc_final: 0.7484 (mp) REVERT: E 443 LYS cc_start: 0.8884 (mmmt) cc_final: 0.8539 (mtpp) REVERT: E 450 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8053 (tm-30) REVERT: E 451 MET cc_start: 0.8440 (tpp) cc_final: 0.7933 (tpt) REVERT: E 466 ARG cc_start: 0.8458 (mtm-85) cc_final: 0.8166 (mpp80) REVERT: E 470 MET cc_start: 0.7817 (mtp) cc_final: 0.6634 (mtp) REVERT: E 500 GLU cc_start: 0.7285 (mp0) cc_final: 0.6978 (mp0) REVERT: E 515 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6640 (pp-130) REVERT: G 443 LYS cc_start: 0.8834 (mmtt) cc_final: 0.8457 (mtpp) REVERT: G 450 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8066 (tm-30) REVERT: G 451 MET cc_start: 0.8422 (tpt) cc_final: 0.8051 (tpt) REVERT: G 458 GLN cc_start: 0.8722 (pt0) cc_final: 0.8328 (pt0) REVERT: G 470 MET cc_start: 0.7470 (mtp) cc_final: 0.7045 (mtp) REVERT: G 500 GLU cc_start: 0.6811 (mp0) cc_final: 0.6547 (mp0) REVERT: H 443 LYS cc_start: 0.8505 (mtpp) cc_final: 0.8238 (ptpt) REVERT: H 444 ARG cc_start: 0.8890 (ttt180) cc_final: 0.8141 (ttt180) REVERT: H 450 GLN cc_start: 0.8861 (tm-30) cc_final: 0.8429 (tm-30) REVERT: H 451 MET cc_start: 0.8247 (tpt) cc_final: 0.7647 (tpt) REVERT: H 457 ASN cc_start: 0.8862 (m-40) cc_final: 0.8054 (t0) REVERT: H 500 GLU cc_start: 0.6718 (mp0) cc_final: 0.6275 (mp0) REVERT: H 515 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6627 (pp-130) REVERT: I 443 LYS cc_start: 0.8900 (mmtt) cc_final: 0.8586 (mtpp) REVERT: I 450 GLN cc_start: 0.8663 (tm-30) cc_final: 0.7818 (tm-30) REVERT: I 451 MET cc_start: 0.8541 (tpp) cc_final: 0.8160 (tpt) REVERT: I 457 ASN cc_start: 0.8795 (m-40) cc_final: 0.8509 (m-40) REVERT: I 469 ILE cc_start: 0.8898 (tp) cc_final: 0.8644 (tt) REVERT: I 470 MET cc_start: 0.7825 (mtp) cc_final: 0.7587 (mtp) REVERT: I 482 THR cc_start: 0.8404 (OUTLIER) cc_final: 0.8134 (t) REVERT: I 500 GLU cc_start: 0.6536 (mp0) cc_final: 0.6180 (mp0) REVERT: I 517 LEU cc_start: 0.7026 (mp) cc_final: 0.6719 (mp) REVERT: J 439 TRP cc_start: 0.8344 (t60) cc_final: 0.7856 (t60) REVERT: J 441 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8298 (mp10) REVERT: J 443 LYS cc_start: 0.8882 (mmtt) cc_final: 0.8416 (mtpp) REVERT: J 444 ARG cc_start: 0.9032 (ttt180) cc_final: 0.8622 (ttt180) REVERT: J 450 GLN cc_start: 0.8840 (tm-30) cc_final: 0.8046 (tm-30) REVERT: J 451 MET cc_start: 0.8317 (tpt) cc_final: 0.7889 (tpt) REVERT: J 457 ASN cc_start: 0.8779 (m-40) cc_final: 0.8475 (m-40) REVERT: J 466 ARG cc_start: 0.8398 (mpp-170) cc_final: 0.8181 (mtm-85) REVERT: J 470 MET cc_start: 0.7541 (mtp) cc_final: 0.7240 (mtp) REVERT: J 473 ASP cc_start: 0.8580 (p0) cc_final: 0.8168 (p0) REVERT: J 500 GLU cc_start: 0.6301 (mp0) cc_final: 0.6036 (mp0) outliers start: 59 outliers final: 37 residues processed: 372 average time/residue: 0.1980 time to fit residues: 94.9381 Evaluate side-chains 398 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 348 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain F residue 453 GLU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 509 LEU Chi-restraints excluded: chain A residue 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 491 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 489 GLN Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 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 460 LEU Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain E residue 453 GLU Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 515 MET Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain H residue 453 GLU Chi-restraints excluded: chain H residue 482 THR Chi-restraints excluded: chain H residue 504 VAL 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 504 VAL 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 69 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 77 optimal weight: 0.0570 chunk 64 optimal weight: 0.8980 chunk 35 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 overall best weight: 2.7302 ------------------------------------------------------------------------------- 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** A 438 GLN ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 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** G 457 ASN H 438 GLN ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 438 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6930 Z= 0.186 Angle : 0.843 11.629 9300 Z= 0.385 Chirality : 0.044 0.163 1100 Planarity : 0.003 0.017 1190 Dihedral : 5.307 14.848 900 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 7.47 % Allowed : 20.00 % 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: -4.24 (0.24), residues: 840 helix: -2.70 (0.18), residues: 610 sheet: None (None), residues: 0 loop : -2.45 (0.34), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 439 PHE 0.017 0.004 PHE H 501 TYR 0.009 0.001 TYR I 474 ARG 0.006 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 427 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 368 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 439 TRP cc_start: 0.8276 (t60) cc_final: 0.7814 (t60) REVERT: F 443 LYS cc_start: 0.8945 (mmtt) cc_final: 0.8458 (mtpp) REVERT: F 444 ARG cc_start: 0.9047 (ttt180) cc_final: 0.8776 (ttt180) REVERT: F 450 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8103 (tm-30) REVERT: F 457 ASN cc_start: 0.9230 (m-40) cc_final: 0.8896 (m110) REVERT: F 458 GLN cc_start: 0.8521 (pt0) cc_final: 0.8246 (pt0) REVERT: F 474 TYR cc_start: 0.7203 (t80) cc_final: 0.6845 (t80) REVERT: F 482 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8087 (t) REVERT: F 500 GLU cc_start: 0.6639 (mp0) cc_final: 0.6263 (mp0) REVERT: F 515 MET cc_start: 0.7006 (OUTLIER) cc_final: 0.5958 (pp-130) REVERT: A 437 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.6878 (mt0) REVERT: A 441 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7201 (tm-30) REVERT: A 443 LYS cc_start: 0.8846 (mtpt) cc_final: 0.8391 (mtpp) REVERT: A 450 GLN cc_start: 0.8527 (tm-30) cc_final: 0.7535 (tm-30) REVERT: A 451 MET cc_start: 0.8265 (tpt) cc_final: 0.7763 (tpt) REVERT: A 458 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7257 (pt0) REVERT: A 469 ILE cc_start: 0.8916 (tp) cc_final: 0.8605 (tt) REVERT: A 473 ASP cc_start: 0.8483 (p0) cc_final: 0.8153 (p0) REVERT: A 482 THR cc_start: 0.8172 (t) cc_final: 0.7822 (t) REVERT: A 500 GLU cc_start: 0.6482 (mp0) cc_final: 0.6146 (mp0) REVERT: A 501 PHE cc_start: 0.8780 (t80) cc_final: 0.8417 (t80) REVERT: A 503 LYS cc_start: 0.8272 (ptmt) cc_final: 0.8067 (ptmt) REVERT: A 515 MET cc_start: 0.6892 (OUTLIER) cc_final: 0.6423 (pp-130) REVERT: B 443 LYS cc_start: 0.9026 (mmtt) cc_final: 0.8635 (mtpp) REVERT: B 450 GLN cc_start: 0.8423 (tm-30) cc_final: 0.7575 (tm-30) REVERT: B 451 MET cc_start: 0.8062 (tpt) cc_final: 0.7506 (tpt) REVERT: B 458 GLN cc_start: 0.8540 (pt0) cc_final: 0.8253 (pt0) REVERT: B 469 ILE cc_start: 0.9050 (tp) cc_final: 0.8792 (tt) REVERT: B 482 THR cc_start: 0.7809 (t) cc_final: 0.7424 (t) REVERT: C 443 LYS cc_start: 0.8965 (mmtt) cc_final: 0.8515 (mtpp) REVERT: C 450 GLN cc_start: 0.8645 (tm-30) cc_final: 0.8080 (tm-30) REVERT: C 458 GLN cc_start: 0.8055 (pt0) cc_final: 0.7142 (pt0) REVERT: C 469 ILE cc_start: 0.8874 (tp) cc_final: 0.8598 (tt) REVERT: C 482 THR cc_start: 0.8203 (t) cc_final: 0.7860 (t) REVERT: C 488 ARG cc_start: 0.8466 (mtm180) cc_final: 0.8066 (mtm180) REVERT: C 500 GLU cc_start: 0.6895 (mp0) cc_final: 0.6626 (mp0) REVERT: D 443 LYS cc_start: 0.8874 (mmtt) cc_final: 0.8599 (mtpp) REVERT: D 450 GLN cc_start: 0.8460 (tm-30) cc_final: 0.7391 (tm-30) REVERT: D 474 TYR cc_start: 0.7660 (t80) cc_final: 0.6994 (t80) REVERT: D 515 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6538 (pp-130) REVERT: D 517 LEU cc_start: 0.7667 (mt) cc_final: 0.7189 (mp) REVERT: E 444 ARG cc_start: 0.8797 (ttt180) cc_final: 0.8340 (ttt180) REVERT: E 450 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8063 (tm-30) REVERT: E 451 MET cc_start: 0.8458 (tpp) cc_final: 0.7960 (tpt) REVERT: E 470 MET cc_start: 0.7613 (mtp) cc_final: 0.6029 (mtp) REVERT: E 472 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.5557 (pp20) REVERT: E 500 GLU cc_start: 0.7207 (mp0) cc_final: 0.6898 (mp0) REVERT: E 515 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.6619 (pp-130) REVERT: G 443 LYS cc_start: 0.8796 (mmtt) cc_final: 0.8483 (mtpp) REVERT: G 450 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8287 (tm-30) REVERT: G 451 MET cc_start: 0.8386 (tpt) cc_final: 0.8051 (tpt) REVERT: G 458 GLN cc_start: 0.8722 (pt0) cc_final: 0.8393 (pt0) REVERT: G 470 MET cc_start: 0.7517 (mtp) cc_final: 0.6644 (mtp) REVERT: G 500 GLU cc_start: 0.6725 (mp0) cc_final: 0.6479 (mp0) REVERT: H 444 ARG cc_start: 0.8884 (ttt180) cc_final: 0.7940 (ttt180) REVERT: H 450 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8375 (tm-30) REVERT: H 451 MET cc_start: 0.8289 (tpt) cc_final: 0.7675 (tpt) REVERT: H 457 ASN cc_start: 0.8872 (m-40) cc_final: 0.8098 (t0) REVERT: H 458 GLN cc_start: 0.8884 (pt0) cc_final: 0.8414 (pt0) REVERT: H 470 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7419 (mtt) REVERT: H 492 ASP cc_start: 0.8421 (p0) cc_final: 0.8122 (m-30) REVERT: H 500 GLU cc_start: 0.6710 (mp0) cc_final: 0.6280 (mp0) REVERT: H 515 MET cc_start: 0.7101 (OUTLIER) cc_final: 0.6525 (pp-130) REVERT: H 517 LEU cc_start: 0.6889 (mp) cc_final: 0.6510 (mp) REVERT: I 443 LYS cc_start: 0.8886 (mmtt) cc_final: 0.8564 (mtpp) REVERT: I 451 MET cc_start: 0.8555 (tpp) cc_final: 0.7315 (ttm) REVERT: I 457 ASN cc_start: 0.8705 (m-40) cc_final: 0.8267 (t0) REVERT: I 469 ILE cc_start: 0.8810 (tp) cc_final: 0.8603 (tt) REVERT: I 470 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7288 (mmm) REVERT: I 482 THR cc_start: 0.8324 (t) cc_final: 0.8072 (t) REVERT: I 500 GLU cc_start: 0.6870 (mp0) cc_final: 0.6413 (mp0) REVERT: J 439 TRP cc_start: 0.8239 (t60) cc_final: 0.7862 (t60) REVERT: J 441 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8299 (mp10) REVERT: J 443 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8387 (mtpp) REVERT: J 444 ARG cc_start: 0.8978 (ttt180) cc_final: 0.8654 (ttt180) REVERT: J 451 MET cc_start: 0.8306 (tpt) cc_final: 0.7635 (ttt) REVERT: J 453 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8108 (pp20) REVERT: J 457 ASN cc_start: 0.8732 (m-40) cc_final: 0.8035 (t0) REVERT: J 470 MET cc_start: 0.7532 (mtp) cc_final: 0.7177 (mtp) REVERT: J 473 ASP cc_start: 0.8551 (p0) cc_final: 0.8150 (p0) REVERT: J 500 GLU cc_start: 0.6359 (mp0) cc_final: 0.6081 (mp0) outliers start: 59 outliers final: 30 residues processed: 379 average time/residue: 0.2158 time to fit residues: 102.6802 Evaluate side-chains 396 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 352 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 F residue 509 LEU 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 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 A residue 515 MET Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 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 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 491 LEU 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 515 MET Chi-restraints excluded: chain I residue 453 GLU Chi-restraints excluded: chain I residue 470 MET Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain I residue 504 VAL 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 8 optimal weight: 20.0000 chunk 44 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 48 optimal weight: 0.0030 chunk 47 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 overall best weight: 5.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 438 GLN ** F 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 489 GLN ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 GLN ** E 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 457 ASN I 438 GLN ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6930 Z= 0.258 Angle : 0.900 11.771 9300 Z= 0.412 Chirality : 0.047 0.176 1100 Planarity : 0.003 0.048 1190 Dihedral : 5.557 14.971 900 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 7.22 % Allowed : 22.41 % Favored : 70.38 % 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: -3.72 (0.26), residues: 840 helix: -2.51 (0.19), residues: 590 sheet: None (None), residues: 0 loop : -1.77 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 439 PHE 0.027 0.004 PHE H 501 TYR 0.007 0.002 TYR I 474 ARG 0.010 0.001 ARG B 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 421 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 364 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 439 TRP cc_start: 0.8297 (t60) cc_final: 0.7639 (t60) REVERT: F 443 LYS cc_start: 0.8962 (mmtt) cc_final: 0.8497 (mtpp) REVERT: F 444 ARG cc_start: 0.9059 (ttt180) cc_final: 0.8781 (ttt180) REVERT: F 450 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8072 (tm-30) REVERT: F 457 ASN cc_start: 0.9207 (m-40) cc_final: 0.8984 (m-40) REVERT: F 458 GLN cc_start: 0.8444 (pt0) cc_final: 0.7866 (pt0) REVERT: F 469 ILE cc_start: 0.8675 (tp) cc_final: 0.8351 (tt) REVERT: F 500 GLU cc_start: 0.6612 (mp0) cc_final: 0.6321 (mp0) REVERT: F 515 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6073 (pp-130) REVERT: A 437 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7020 (mt0) REVERT: A 441 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7242 (tm-30) REVERT: A 443 LYS cc_start: 0.8962 (mtpt) cc_final: 0.8532 (mtpp) REVERT: A 450 GLN cc_start: 0.8582 (tm-30) cc_final: 0.7561 (tm-30) REVERT: A 451 MET cc_start: 0.8321 (tpt) cc_final: 0.7731 (tpt) REVERT: A 458 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7410 (pt0) REVERT: A 469 ILE cc_start: 0.8945 (tp) cc_final: 0.8628 (tt) REVERT: A 473 ASP cc_start: 0.8501 (p0) cc_final: 0.8217 (p0) REVERT: A 482 THR cc_start: 0.8304 (t) cc_final: 0.7974 (t) REVERT: A 501 PHE cc_start: 0.8765 (t80) cc_final: 0.8503 (t80) REVERT: A 515 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6687 (pp-130) REVERT: B 443 LYS cc_start: 0.9130 (mmtt) cc_final: 0.8697 (mtpp) REVERT: B 450 GLN cc_start: 0.8452 (tm-30) cc_final: 0.7526 (tm-30) REVERT: B 451 MET cc_start: 0.8169 (tpt) cc_final: 0.7627 (tpt) REVERT: B 482 THR cc_start: 0.7904 (t) cc_final: 0.7537 (t) REVERT: C 443 LYS cc_start: 0.8985 (mmtt) cc_final: 0.8503 (mtpp) REVERT: C 450 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8050 (tm-30) REVERT: C 458 GLN cc_start: 0.8205 (pt0) cc_final: 0.7225 (pt0) REVERT: C 466 ARG cc_start: 0.8707 (mpp-170) cc_final: 0.8502 (mpp80) REVERT: C 469 ILE cc_start: 0.8943 (tp) cc_final: 0.8643 (tt) REVERT: C 482 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.8028 (t) REVERT: C 488 ARG cc_start: 0.8512 (mtm180) cc_final: 0.8139 (mtm180) REVERT: C 515 MET cc_start: 0.6725 (pp-130) cc_final: 0.6524 (pp-130) REVERT: D 443 LYS cc_start: 0.8935 (mmtt) cc_final: 0.8638 (mtpp) REVERT: D 445 GLU cc_start: 0.8313 (tp30) cc_final: 0.7835 (tp30) REVERT: D 450 GLN cc_start: 0.8454 (tm-30) cc_final: 0.7420 (tm-30) REVERT: D 515 MET cc_start: 0.7149 (OUTLIER) cc_final: 0.6882 (pp-130) REVERT: E 443 LYS cc_start: 0.8848 (mmmt) cc_final: 0.8592 (mtpp) REVERT: E 444 ARG cc_start: 0.8797 (ttt180) cc_final: 0.8596 (ttt180) REVERT: E 450 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8063 (tm-30) REVERT: E 451 MET cc_start: 0.8401 (tpp) cc_final: 0.7934 (tpt) REVERT: E 470 MET cc_start: 0.7700 (mtp) cc_final: 0.6672 (mtp) REVERT: E 500 GLU cc_start: 0.7237 (mp0) cc_final: 0.6954 (mp0) REVERT: E 518 GLN cc_start: 0.8271 (tm-30) cc_final: 0.7878 (tm-30) REVERT: G 443 LYS cc_start: 0.8816 (mmtt) cc_final: 0.8480 (mtpp) REVERT: G 450 GLN cc_start: 0.8834 (tm-30) cc_final: 0.8025 (tm-30) REVERT: G 451 MET cc_start: 0.8451 (tpt) cc_final: 0.8017 (tpt) REVERT: G 458 GLN cc_start: 0.8770 (pt0) cc_final: 0.8464 (pt0) REVERT: G 500 GLU cc_start: 0.6797 (mp0) cc_final: 0.6548 (mp0) REVERT: H 444 ARG cc_start: 0.8819 (ttt180) cc_final: 0.7985 (ttt180) REVERT: H 450 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8376 (tm-30) REVERT: H 451 MET cc_start: 0.8405 (tpt) cc_final: 0.7673 (tpt) REVERT: H 457 ASN cc_start: 0.8931 (m-40) cc_final: 0.8129 (t0) REVERT: H 458 GLN cc_start: 0.8942 (pt0) cc_final: 0.8455 (pt0) REVERT: H 470 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7600 (mtt) REVERT: H 500 GLU cc_start: 0.6784 (mp0) cc_final: 0.6323 (mp0) REVERT: H 515 MET cc_start: 0.7251 (OUTLIER) cc_final: 0.6725 (pp-130) REVERT: I 443 LYS cc_start: 0.8924 (mmtt) cc_final: 0.8417 (mmmm) REVERT: I 450 GLN cc_start: 0.8673 (tm-30) cc_final: 0.7775 (tm-30) REVERT: I 451 MET cc_start: 0.8544 (tpp) cc_final: 0.7330 (ttm) REVERT: I 457 ASN cc_start: 0.8876 (m-40) cc_final: 0.8590 (m-40) REVERT: I 469 ILE cc_start: 0.8799 (tp) cc_final: 0.8527 (tt) REVERT: I 470 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.7076 (mmm) REVERT: I 473 ASP cc_start: 0.8534 (p0) cc_final: 0.8200 (p0) REVERT: I 482 THR cc_start: 0.8428 (t) cc_final: 0.8170 (t) REVERT: I 500 GLU cc_start: 0.6834 (mp0) cc_final: 0.6380 (mp0) REVERT: J 441 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8336 (mp10) REVERT: J 443 LYS cc_start: 0.8893 (mmtt) cc_final: 0.8441 (mtpp) REVERT: J 444 ARG cc_start: 0.9028 (ttt180) cc_final: 0.8708 (ttt180) REVERT: J 450 GLN cc_start: 0.8876 (tm-30) cc_final: 0.7958 (tm-30) REVERT: J 451 MET cc_start: 0.8158 (tpt) cc_final: 0.7432 (ttt) REVERT: J 457 ASN cc_start: 0.8756 (m-40) cc_final: 0.8041 (t0) REVERT: J 470 MET cc_start: 0.7691 (mtp) cc_final: 0.6972 (mtp) REVERT: J 473 ASP cc_start: 0.8555 (p0) cc_final: 0.8144 (p0) REVERT: J 500 GLU cc_start: 0.6456 (mp0) cc_final: 0.6157 (mp0) outliers start: 57 outliers final: 42 residues processed: 377 average time/residue: 0.2163 time to fit residues: 103.3517 Evaluate side-chains 410 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 357 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 438 GLN Chi-restraints excluded: chain F residue 453 GLU Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 509 LEU 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 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 A residue 515 MET Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 489 GLN Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 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 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 G residue 448 VAL Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain H residue 453 GLU Chi-restraints excluded: chain H residue 470 MET 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 470 MET Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain I residue 504 VAL Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain J residue 453 GLU Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 504 VAL 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 23 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 438 GLN ** F 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN D 489 GLN E 438 GLN ** E 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6930 Z= 0.212 Angle : 0.917 13.149 9300 Z= 0.413 Chirality : 0.046 0.172 1100 Planarity : 0.003 0.041 1190 Dihedral : 5.391 15.016 900 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 7.59 % Allowed : 23.29 % Favored : 69.11 % 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: -3.50 (0.27), residues: 840 helix: -2.34 (0.19), residues: 590 sheet: None (None), residues: 0 loop : -1.70 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 439 PHE 0.025 0.004 PHE H 501 TYR 0.009 0.001 TYR I 474 ARG 0.009 0.001 ARG J 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 409 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 349 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 439 TRP cc_start: 0.8254 (t60) cc_final: 0.7783 (t60) REVERT: F 444 ARG cc_start: 0.9031 (ttt180) cc_final: 0.8762 (ttt180) REVERT: F 450 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8127 (tm-30) REVERT: F 457 ASN cc_start: 0.9103 (m-40) cc_final: 0.8863 (m110) REVERT: F 458 GLN cc_start: 0.8515 (pt0) cc_final: 0.7935 (pt0) REVERT: F 469 ILE cc_start: 0.8723 (tp) cc_final: 0.8340 (tt) REVERT: F 470 MET cc_start: 0.7740 (mtp) cc_final: 0.7054 (mtp) REVERT: F 500 GLU cc_start: 0.6614 (mp0) cc_final: 0.6314 (mp0) REVERT: F 515 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6052 (pp-130) REVERT: A 437 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.6993 (mt0) REVERT: A 441 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7185 (tm-30) REVERT: A 443 LYS cc_start: 0.8867 (mtpt) cc_final: 0.8478 (mtpp) REVERT: A 450 GLN cc_start: 0.8581 (tm-30) cc_final: 0.7424 (tm-30) REVERT: A 451 MET cc_start: 0.8303 (tpt) cc_final: 0.7732 (tpt) REVERT: A 458 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7239 (pt0) REVERT: A 466 ARG cc_start: 0.8287 (mtm-85) cc_final: 0.7862 (mtm-85) REVERT: A 469 ILE cc_start: 0.8908 (tp) cc_final: 0.8618 (tt) REVERT: A 473 ASP cc_start: 0.8480 (p0) cc_final: 0.8188 (p0) REVERT: A 482 THR cc_start: 0.8261 (t) cc_final: 0.7917 (t) REVERT: A 500 GLU cc_start: 0.6411 (mp0) cc_final: 0.6122 (mp0) REVERT: A 501 PHE cc_start: 0.8688 (t80) cc_final: 0.8480 (t80) REVERT: A 515 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.6899 (pp-130) REVERT: B 437 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7347 (tt0) REVERT: B 443 LYS cc_start: 0.9108 (mmtt) cc_final: 0.8666 (mtpp) REVERT: B 450 GLN cc_start: 0.8332 (tm-30) cc_final: 0.7413 (tm-30) REVERT: B 451 MET cc_start: 0.8161 (tpt) cc_final: 0.7653 (tpt) REVERT: B 482 THR cc_start: 0.7851 (t) cc_final: 0.7512 (t) REVERT: C 443 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8499 (mtpp) REVERT: C 450 GLN cc_start: 0.8731 (tm-30) cc_final: 0.7956 (tm-30) REVERT: C 458 GLN cc_start: 0.8165 (pt0) cc_final: 0.7101 (pt0) REVERT: C 469 ILE cc_start: 0.8891 (tp) cc_final: 0.8624 (tt) REVERT: C 482 THR cc_start: 0.8217 (OUTLIER) cc_final: 0.7925 (t) REVERT: C 488 ARG cc_start: 0.8488 (mtm180) cc_final: 0.8081 (mtm180) REVERT: D 443 LYS cc_start: 0.8904 (mmtt) cc_final: 0.8615 (mtpp) REVERT: D 450 GLN cc_start: 0.8483 (tm-30) cc_final: 0.7435 (tm-30) REVERT: D 458 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7388 (pt0) REVERT: D 515 MET cc_start: 0.6952 (OUTLIER) cc_final: 0.6622 (pp-130) REVERT: E 443 LYS cc_start: 0.8818 (mmmt) cc_final: 0.8542 (mtpp) REVERT: E 450 GLN cc_start: 0.8758 (tm-30) cc_final: 0.8098 (tm-30) REVERT: E 451 MET cc_start: 0.8416 (tpp) cc_final: 0.7917 (tpt) REVERT: E 470 MET cc_start: 0.7662 (mtp) cc_final: 0.6074 (mtp) REVERT: E 472 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.5664 (pp20) REVERT: E 482 THR cc_start: 0.8367 (t) cc_final: 0.8007 (t) REVERT: E 500 GLU cc_start: 0.7212 (mp0) cc_final: 0.6951 (mp0) REVERT: G 443 LYS cc_start: 0.8749 (mmtt) cc_final: 0.8442 (mtpp) REVERT: G 450 GLN cc_start: 0.8811 (tm-30) cc_final: 0.7971 (tm-30) REVERT: G 451 MET cc_start: 0.8421 (tpt) cc_final: 0.8077 (tpt) REVERT: G 458 GLN cc_start: 0.8762 (pt0) cc_final: 0.8421 (pt0) REVERT: G 500 GLU cc_start: 0.6759 (mp0) cc_final: 0.6511 (mp0) REVERT: H 444 ARG cc_start: 0.8689 (ttt180) cc_final: 0.8411 (ttt180) REVERT: H 450 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8391 (tm-30) REVERT: H 451 MET cc_start: 0.8398 (tpt) cc_final: 0.7635 (tpt) REVERT: H 457 ASN cc_start: 0.8825 (m-40) cc_final: 0.8161 (t0) REVERT: H 458 GLN cc_start: 0.8896 (pt0) cc_final: 0.8402 (pt0) REVERT: H 470 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7593 (mtp) REVERT: H 500 GLU cc_start: 0.6810 (mp0) cc_final: 0.6350 (mp0) REVERT: H 515 MET cc_start: 0.7193 (OUTLIER) cc_final: 0.6747 (pp-130) REVERT: I 443 LYS cc_start: 0.8872 (mmtt) cc_final: 0.8378 (mmmm) REVERT: I 450 GLN cc_start: 0.8629 (tm-30) cc_final: 0.7693 (tm-30) REVERT: I 451 MET cc_start: 0.8559 (tpp) cc_final: 0.7306 (ttm) REVERT: I 457 ASN cc_start: 0.8875 (m-40) cc_final: 0.8339 (t0) REVERT: I 469 ILE cc_start: 0.8768 (tp) cc_final: 0.8566 (tt) REVERT: I 470 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.7176 (mmm) REVERT: I 482 THR cc_start: 0.8379 (t) cc_final: 0.8150 (t) REVERT: I 500 GLU cc_start: 0.6860 (mp0) cc_final: 0.6404 (mp0) REVERT: J 441 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8324 (mp10) REVERT: J 443 LYS cc_start: 0.8842 (mmtt) cc_final: 0.8447 (mtpp) REVERT: J 444 ARG cc_start: 0.8929 (ttt180) cc_final: 0.8633 (ttt180) REVERT: J 450 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8015 (tm-30) REVERT: J 451 MET cc_start: 0.8238 (tpt) cc_final: 0.7571 (ttt) REVERT: J 457 ASN cc_start: 0.8717 (m-40) cc_final: 0.8074 (t0) REVERT: J 466 ARG cc_start: 0.8112 (mtm-85) cc_final: 0.7870 (mtm-85) REVERT: J 470 MET cc_start: 0.7485 (mtp) cc_final: 0.6698 (mtp) REVERT: J 473 ASP cc_start: 0.8538 (p0) cc_final: 0.8082 (p0) REVERT: J 500 GLU cc_start: 0.6341 (mp0) cc_final: 0.6042 (mp0) outliers start: 60 outliers final: 42 residues processed: 364 average time/residue: 0.2091 time to fit residues: 96.3365 Evaluate side-chains 396 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 340 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 438 GLN Chi-restraints excluded: chain F residue 453 GLU Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 509 LEU Chi-restraints excluded: chain 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 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 A residue 515 MET Chi-restraints excluded: chain B residue 437 GLN Chi-restraints excluded: chain B residue 440 ILE 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 509 LEU Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 494 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 458 GLN Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain E residue 438 GLN 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 509 LEU Chi-restraints excluded: chain G residue 448 VAL Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain G residue 509 LEU Chi-restraints excluded: chain H residue 453 GLU Chi-restraints excluded: chain H residue 470 MET 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 470 MET Chi-restraints excluded: chain I residue 504 VAL Chi-restraints excluded: chain I residue 509 LEU Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain J residue 453 GLU Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 504 VAL 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 71 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 64 optimal weight: 9.9990 chunk 67 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 75 optimal weight: 0.4980 chunk 46 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 438 GLN ** F 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** B 489 GLN ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 514 GLN ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6930 Z= 0.193 Angle : 0.916 12.696 9300 Z= 0.413 Chirality : 0.044 0.165 1100 Planarity : 0.003 0.031 1190 Dihedral : 5.235 18.209 900 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 6.46 % Allowed : 25.06 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.25), residues: 840 helix: -2.31 (0.19), residues: 610 sheet: None (None), residues: 0 loop : -2.40 (0.35), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 439 PHE 0.017 0.003 PHE H 501 TYR 0.009 0.001 TYR I 474 ARG 0.008 0.001 ARG D 483 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 345 time to evaluate : 0.854 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 439 TRP cc_start: 0.8118 (t60) cc_final: 0.7617 (t60) REVERT: F 443 LYS cc_start: 0.8937 (mmtt) cc_final: 0.8486 (mtpp) REVERT: F 450 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8159 (tm-30) REVERT: F 457 ASN cc_start: 0.9078 (m-40) cc_final: 0.8762 (m110) REVERT: F 458 GLN cc_start: 0.8477 (pt0) cc_final: 0.8017 (pt0) REVERT: F 469 ILE cc_start: 0.8576 (tp) cc_final: 0.8218 (tt) REVERT: F 470 MET cc_start: 0.7463 (mtp) cc_final: 0.6974 (mtp) REVERT: F 500 GLU cc_start: 0.6619 (mp0) cc_final: 0.6353 (mp0) REVERT: F 515 MET cc_start: 0.6974 (pp-130) cc_final: 0.5951 (pp-130) REVERT: A 437 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.6974 (mt0) REVERT: A 441 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7194 (tm-30) REVERT: A 443 LYS cc_start: 0.8868 (mtpt) cc_final: 0.8502 (mtpp) REVERT: A 450 GLN cc_start: 0.8637 (tm-30) cc_final: 0.7699 (tm-30) REVERT: A 451 MET cc_start: 0.8233 (tpt) cc_final: 0.7806 (tpt) REVERT: A 458 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7041 (pt0) REVERT: A 469 ILE cc_start: 0.8917 (tp) cc_final: 0.8647 (tt) REVERT: A 473 ASP cc_start: 0.8468 (p0) cc_final: 0.8172 (p0) REVERT: A 482 THR cc_start: 0.8206 (t) cc_final: 0.7883 (t) REVERT: A 501 PHE cc_start: 0.8594 (t80) cc_final: 0.8369 (t80) REVERT: A 515 MET cc_start: 0.7088 (OUTLIER) cc_final: 0.6637 (pp-130) REVERT: B 440 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.8956 (mt) REVERT: B 443 LYS cc_start: 0.8970 (mmtt) cc_final: 0.8574 (mtpp) REVERT: B 450 GLN cc_start: 0.8392 (tm-30) cc_final: 0.7411 (tm-30) REVERT: B 451 MET cc_start: 0.8167 (tpt) cc_final: 0.7715 (tpt) REVERT: B 482 THR cc_start: 0.8212 (t) cc_final: 0.7877 (t) REVERT: C 443 LYS cc_start: 0.8769 (mmtt) cc_final: 0.8367 (mtpp) REVERT: C 450 GLN cc_start: 0.8617 (tm-30) cc_final: 0.7888 (tm-30) REVERT: C 458 GLN cc_start: 0.7919 (pt0) cc_final: 0.6996 (pt0) REVERT: C 461 ASP cc_start: 0.8916 (t70) cc_final: 0.8687 (t0) REVERT: C 488 ARG cc_start: 0.8411 (mtm180) cc_final: 0.7978 (mtm180) REVERT: D 443 LYS cc_start: 0.8863 (mmtt) cc_final: 0.8615 (mtpp) REVERT: D 445 GLU cc_start: 0.8290 (tp30) cc_final: 0.7772 (tp30) REVERT: D 450 GLN cc_start: 0.8553 (tm-30) cc_final: 0.8139 (tm-30) REVERT: D 451 MET cc_start: 0.7889 (tpt) cc_final: 0.7681 (tpt) REVERT: D 461 ASP cc_start: 0.8971 (t0) cc_final: 0.8530 (t0) REVERT: D 515 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.6393 (pp-130) REVERT: E 443 LYS cc_start: 0.8816 (mmmt) cc_final: 0.8583 (mtpp) REVERT: E 450 GLN cc_start: 0.8523 (tm-30) cc_final: 0.7913 (tm-30) REVERT: E 451 MET cc_start: 0.8358 (tpp) cc_final: 0.7909 (tpt) REVERT: E 470 MET cc_start: 0.7657 (mtp) cc_final: 0.5870 (mtp) REVERT: E 472 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.5598 (pp20) REVERT: E 488 ARG cc_start: 0.8845 (mtm180) cc_final: 0.8618 (mtm180) REVERT: E 500 GLU cc_start: 0.7034 (mp0) cc_final: 0.6816 (mp0) REVERT: G 443 LYS cc_start: 0.8717 (mmtt) cc_final: 0.8374 (mtpp) REVERT: G 450 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8018 (tm-30) REVERT: G 451 MET cc_start: 0.8301 (tpt) cc_final: 0.8007 (tpt) REVERT: G 458 GLN cc_start: 0.8727 (pt0) cc_final: 0.8428 (pt0) REVERT: G 500 GLU cc_start: 0.6875 (mp0) cc_final: 0.6637 (mp0) REVERT: G 515 MET cc_start: 0.6977 (pp-130) cc_final: 0.6529 (pp-130) REVERT: H 450 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8377 (tm-30) REVERT: H 451 MET cc_start: 0.8379 (tpt) cc_final: 0.7486 (tpt) REVERT: H 457 ASN cc_start: 0.8801 (m-40) cc_final: 0.8304 (t0) REVERT: H 458 GLN cc_start: 0.8868 (pt0) cc_final: 0.8407 (pt0) REVERT: H 500 GLU cc_start: 0.6677 (mp0) cc_final: 0.6363 (mp0) REVERT: I 443 LYS cc_start: 0.8857 (mmtt) cc_final: 0.8348 (mmmm) REVERT: I 450 GLN cc_start: 0.8552 (tm-30) cc_final: 0.7533 (tm-30) REVERT: I 451 MET cc_start: 0.8489 (tpp) cc_final: 0.7355 (ttm) REVERT: I 457 ASN cc_start: 0.8810 (m-40) cc_final: 0.8321 (t0) REVERT: I 482 THR cc_start: 0.8301 (t) cc_final: 0.8068 (t) REVERT: I 488 ARG cc_start: 0.8718 (mtm180) cc_final: 0.8459 (mtm180) REVERT: I 500 GLU cc_start: 0.6824 (mp0) cc_final: 0.6389 (mp0) REVERT: J 441 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8435 (mp10) REVERT: J 443 LYS cc_start: 0.8772 (mmtt) cc_final: 0.8410 (mtpp) REVERT: J 444 ARG cc_start: 0.8885 (ttt180) cc_final: 0.8572 (ttt180) REVERT: J 451 MET cc_start: 0.8166 (tpt) cc_final: 0.7702 (ttt) REVERT: J 457 ASN cc_start: 0.8643 (m-40) cc_final: 0.8269 (t0) REVERT: J 500 GLU cc_start: 0.6168 (mp0) cc_final: 0.5896 (mp0) outliers start: 51 outliers final: 40 residues processed: 358 average time/residue: 0.2228 time to fit residues: 100.4366 Evaluate side-chains 378 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 330 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 438 GLN Chi-restraints excluded: chain F residue 504 VAL 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 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 A residue 515 MET Chi-restraints excluded: chain B residue 440 ILE 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 489 GLN Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 458 GLN Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 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 509 LEU 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 453 GLU Chi-restraints excluded: chain H residue 482 THR Chi-restraints excluded: chain H residue 509 LEU Chi-restraints excluded: chain I residue 453 GLU Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain I residue 504 VAL Chi-restraints excluded: chain I residue 509 LEU Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain J residue 453 GLU Chi-restraints excluded: chain J residue 460 LEU Chi-restraints excluded: chain J residue 504 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 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 438 GLN ** F 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 GLN ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 457 ASN ** D 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 438 GLN ** 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 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6930 Z= 0.299 Angle : 0.989 12.794 9300 Z= 0.454 Chirality : 0.048 0.176 1100 Planarity : 0.004 0.063 1190 Dihedral : 5.474 16.061 900 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 5.70 % Allowed : 27.47 % Favored : 66.84 % 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: -3.52 (0.26), residues: 840 helix: -2.42 (0.19), residues: 590 sheet: None (None), residues: 0 loop : -1.53 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP H 439 PHE 0.019 0.005 PHE H 501 TYR 0.009 0.002 TYR D 474 ARG 0.014 0.001 ARG C 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 386 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 341 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 439 TRP cc_start: 0.8211 (t60) cc_final: 0.7718 (t60) REVERT: F 443 LYS cc_start: 0.8952 (mmtt) cc_final: 0.8470 (mtpp) REVERT: F 450 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8225 (tm-30) REVERT: F 451 MET cc_start: 0.8225 (tpp) cc_final: 0.7533 (tpt) REVERT: F 457 ASN cc_start: 0.9111 (m-40) cc_final: 0.8841 (m110) REVERT: F 469 ILE cc_start: 0.8784 (tp) cc_final: 0.8470 (tt) REVERT: F 515 MET cc_start: 0.7219 (OUTLIER) cc_final: 0.6145 (pp-130) REVERT: A 437 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.6980 (mt0) REVERT: A 441 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7243 (tm-30) REVERT: A 443 LYS cc_start: 0.9017 (mtpt) cc_final: 0.8702 (mtpp) REVERT: A 450 GLN cc_start: 0.8659 (tm-30) cc_final: 0.7654 (tm-30) REVERT: A 451 MET cc_start: 0.8182 (tpt) cc_final: 0.7714 (tpt) REVERT: A 453 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8167 (tm-30) REVERT: A 457 ASN cc_start: 0.9096 (OUTLIER) cc_final: 0.8673 (m-40) REVERT: A 458 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7436 (pt0) REVERT: A 469 ILE cc_start: 0.8926 (tp) cc_final: 0.8641 (tt) REVERT: A 473 ASP cc_start: 0.8429 (p0) cc_final: 0.8118 (p0) REVERT: A 482 THR cc_start: 0.8339 (t) cc_final: 0.8008 (t) REVERT: A 501 PHE cc_start: 0.8754 (t80) cc_final: 0.8541 (t80) REVERT: A 515 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.6758 (pp-130) REVERT: B 443 LYS cc_start: 0.9145 (mmtt) cc_final: 0.8689 (mtpp) REVERT: B 450 GLN cc_start: 0.8421 (tm-30) cc_final: 0.7424 (tm-30) REVERT: B 451 MET cc_start: 0.8214 (tpt) cc_final: 0.7692 (tpt) REVERT: B 458 GLN cc_start: 0.8557 (pt0) cc_final: 0.8316 (pt0) REVERT: B 482 THR cc_start: 0.7836 (t) cc_final: 0.7495 (t) REVERT: B 489 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8877 (mm-40) REVERT: C 443 LYS cc_start: 0.8893 (mmtt) cc_final: 0.8427 (mtpp) REVERT: C 450 GLN cc_start: 0.8660 (tm-30) cc_final: 0.7885 (tm-30) REVERT: C 453 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8403 (tm-30) REVERT: C 458 GLN cc_start: 0.8218 (pt0) cc_final: 0.7263 (pt0) REVERT: C 473 ASP cc_start: 0.8601 (p0) cc_final: 0.8377 (p0) REVERT: C 482 THR cc_start: 0.8299 (OUTLIER) cc_final: 0.8074 (t) REVERT: C 488 ARG cc_start: 0.8478 (mtm180) cc_final: 0.8086 (mtm180) REVERT: D 443 LYS cc_start: 0.8913 (mmtt) cc_final: 0.8645 (mtpp) REVERT: D 445 GLU cc_start: 0.8359 (tp30) cc_final: 0.7836 (tp30) REVERT: D 450 GLN cc_start: 0.8563 (tm-30) cc_final: 0.7409 (tm-30) REVERT: D 515 MET cc_start: 0.7059 (OUTLIER) cc_final: 0.6819 (pp-130) REVERT: E 443 LYS cc_start: 0.8816 (mmmt) cc_final: 0.8530 (mtpp) REVERT: E 445 GLU cc_start: 0.8237 (tp30) cc_final: 0.7964 (tp30) REVERT: E 450 GLN cc_start: 0.8865 (tm-30) cc_final: 0.8125 (tm-30) REVERT: E 451 MET cc_start: 0.8385 (tpp) cc_final: 0.7908 (tpt) REVERT: E 458 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7194 (pt0) REVERT: E 470 MET cc_start: 0.7711 (mtp) cc_final: 0.6545 (mtp) REVERT: E 500 GLU cc_start: 0.7181 (mp0) cc_final: 0.6931 (mp0) REVERT: G 443 LYS cc_start: 0.8767 (mmtt) cc_final: 0.8424 (mtpp) REVERT: G 450 GLN cc_start: 0.8749 (tm-30) cc_final: 0.7916 (tm-30) REVERT: G 451 MET cc_start: 0.8467 (tpt) cc_final: 0.7984 (tpt) REVERT: G 458 GLN cc_start: 0.8807 (pt0) cc_final: 0.8482 (pt0) REVERT: G 461 ASP cc_start: 0.8882 (t70) cc_final: 0.8581 (t70) REVERT: G 470 MET cc_start: 0.7691 (mtp) cc_final: 0.7286 (mtp) REVERT: G 500 GLU cc_start: 0.6774 (mp0) cc_final: 0.6511 (mp0) REVERT: G 515 MET cc_start: 0.7041 (pp-130) cc_final: 0.6759 (pp-130) REVERT: H 450 GLN cc_start: 0.8763 (tm-30) cc_final: 0.8385 (tm-30) REVERT: H 451 MET cc_start: 0.8438 (tpt) cc_final: 0.7703 (tpt) REVERT: H 457 ASN cc_start: 0.8930 (m-40) cc_final: 0.8119 (t0) REVERT: H 458 GLN cc_start: 0.8936 (pt0) cc_final: 0.8444 (pt0) REVERT: H 470 MET cc_start: 0.7710 (mtm) cc_final: 0.7491 (mtt) REVERT: H 500 GLU cc_start: 0.6725 (mp0) cc_final: 0.6285 (mp0) REVERT: I 443 LYS cc_start: 0.8935 (mmtt) cc_final: 0.8398 (mmmm) REVERT: I 450 GLN cc_start: 0.8674 (tm-30) cc_final: 0.7755 (tm-30) REVERT: I 451 MET cc_start: 0.8550 (tpp) cc_final: 0.7386 (ttm) REVERT: I 457 ASN cc_start: 0.8922 (m-40) cc_final: 0.8618 (m-40) REVERT: I 473 ASP cc_start: 0.8436 (p0) cc_final: 0.8126 (p0) REVERT: I 482 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8228 (t) REVERT: I 500 GLU cc_start: 0.6800 (mp0) cc_final: 0.6364 (mp0) REVERT: J 441 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8507 (mp10) REVERT: J 443 LYS cc_start: 0.8872 (mmtt) cc_final: 0.8440 (mtpp) REVERT: J 444 ARG cc_start: 0.9000 (ttt180) cc_final: 0.8662 (ttt180) REVERT: J 450 GLN cc_start: 0.8909 (tm-30) cc_final: 0.8003 (tm-30) REVERT: J 451 MET cc_start: 0.8186 (tpt) cc_final: 0.7627 (ttt) REVERT: J 457 ASN cc_start: 0.8730 (m-40) cc_final: 0.8298 (t0) REVERT: J 466 ARG cc_start: 0.8440 (ptp90) cc_final: 0.8050 (mtm-85) REVERT: J 500 GLU cc_start: 0.6094 (mp0) cc_final: 0.5848 (mp0) outliers start: 45 outliers final: 29 residues processed: 353 average time/residue: 0.1915 time to fit residues: 87.4579 Evaluate side-chains 372 residues out of total 790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 329 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 438 GLN 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 448 VAL Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 457 ASN 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 A residue 515 MET Chi-restraints excluded: chain B residue 440 ILE 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 489 GLN 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 491 LEU Chi-restraints excluded: chain C residue 494 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 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 438 GLN Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 504 VAL 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 453 GLU Chi-restraints excluded: chain H residue 482 THR Chi-restraints excluded: chain H residue 509 LEU Chi-restraints excluded: chain I residue 453 GLU Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain J residue 453 GLU Chi-restraints excluded: chain J residue 491 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 3 optimal weight: 0.0070 chunk 45 optimal weight: 5.9990 overall best weight: 3.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 438 GLN ** F 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN ** D 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 438 GLN ** E 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.128958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.115067 restraints weight = 13227.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.118587 restraints weight = 7137.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.121163 restraints weight = 4422.387| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.5620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6930 Z= 0.234 Angle : 0.968 13.264 9300 Z= 0.439 Chirality : 0.047 0.163 1100 Planarity : 0.004 0.053 1190 Dihedral : 5.430 16.439 900 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 6.33 % Allowed : 26.96 % Favored : 66.71 % 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: -3.35 (0.27), residues: 840 helix: -2.17 (0.19), residues: 590 sheet: None (None), residues: 0 loop : -1.83 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 439 PHE 0.020 0.004 PHE H 501 TYR 0.009 0.001 TYR I 474 ARG 0.010 0.001 ARG C 483 =============================================================================== Job complete usr+sys time: 2009.25 seconds wall clock time: 36 minutes 29.09 seconds (2189.09 seconds total)