Starting phenix.real_space_refine on Wed Sep 17 07:37:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ggs_4399/09_2025/6ggs_4399.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ggs_4399/09_2025/6ggs_4399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ggs_4399/09_2025/6ggs_4399.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ggs_4399/09_2025/6ggs_4399.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ggs_4399/09_2025/6ggs_4399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ggs_4399/09_2025/6ggs_4399.map" } resolution = 3.94 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6880 Number of models: 1 Model: "" Number of chains: 1 Chain: "F" 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: A, B, C, D, E, G, H, I, J Time building chain proxies: 1.07, per 1000 atoms: 0.16 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: 0.63 Conformation dependent library (CDL) restraints added in 487.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.28 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: 0.89 Time building geometry restraints manager: 0.83 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: 0.03 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.820 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.460 ------------------------------------------------------------------------------- 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= 0.257 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.003 ARG I 488 TYR 0.005 0.002 TYR H 474 PHE 0.010 0.003 PHE J 501 TRP 0.011 0.003 TRP F 439 Details of bonding type rmsd covalent geometry : bond 0.00571 ( 6930) covalent geometry : angle 1.15445 ( 9300) hydrogen bonds : bond 0.28815 ( 220) hydrogen bonds : angle 8.99325 ( 600) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 399 time to evaluate : 0.329 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: 0.7335 (t60) REVERT: F 443 LYS cc_start: 0.8792 (mmtt) cc_final: 0.8444 (mtpp) REVERT: F 453 GLU cc_start: 0.8492 (pp20) cc_final: 0.8062 (pp20) REVERT: F 457 ASN cc_start: 0.9153 (m110) cc_final: 0.8675 (m-40) REVERT: F 458 GLN cc_start: 0.8384 (pt0) cc_final: 0.8131 (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: 0.6845 (t60) REVERT: A 453 GLU cc_start: 0.8477 (pp20) cc_final: 0.8010 (pp20) REVERT: A 457 ASN cc_start: 0.9084 (m110) cc_final: 0.8775 (m-40) REVERT: A 458 GLN cc_start: 0.8530 (pt0) cc_final: 0.8053 (pt0) REVERT: A 500 GLU cc_start: 0.6342 (mp0) cc_final: 0.6046 (mp0) REVERT: A 515 MET cc_start: 0.7258 (pp-130) cc_final: 0.6721 (pp-130) REVERT: B 443 LYS cc_start: 0.9008 (mmtt) cc_final: 0.8593 (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: 0.8715 (m110) REVERT: B 458 GLN cc_start: 0.8635 (pt0) cc_final: 0.8251 (pt0) REVERT: B 482 THR cc_start: 0.8265 (t) cc_final: 0.7977 (t) REVERT: B 515 MET cc_start: 0.7310 (pp-130) cc_final: 0.6793 (pp-130) REVERT: C 439 TRP cc_start: 0.8076 (t60) cc_final: 0.7602 (t60) REVERT: C 443 LYS cc_start: 0.8824 (mmtt) cc_final: 0.8336 (mtpp) REVERT: C 453 GLU cc_start: 0.8445 (pp20) cc_final: 0.7963 (pp20) REVERT: C 457 ASN cc_start: 0.9178 (m110) cc_final: 0.8949 (m-40) REVERT: C 473 ASP cc_start: 0.8418 (p0) cc_final: 0.7771 (p0) REVERT: C 515 MET cc_start: 0.7031 (pp-130) cc_final: 0.6795 (pp-130) REVERT: D 439 TRP cc_start: 0.8126 (t60) cc_final: 0.7520 (t60) REVERT: D 443 LYS cc_start: 0.8878 (mmtt) cc_final: 0.8497 (mtpp) REVERT: D 453 GLU cc_start: 0.8430 (pp20) cc_final: 0.8010 (pp20) REVERT: D 457 ASN cc_start: 0.9228 (m110) cc_final: 0.8781 (m-40) REVERT: D 461 ASP cc_start: 0.8391 (t70) cc_final: 0.7957 (t70) REVERT: D 473 ASP cc_start: 0.8356 (p0) cc_final: 0.8091 (p0) REVERT: D 515 MET cc_start: 0.7345 (pp-130) cc_final: 0.6830 (pp-130) REVERT: E 439 TRP cc_start: 0.8012 (t60) cc_final: 0.7518 (t60) REVERT: E 443 LYS cc_start: 0.8830 (mmtt) cc_final: 0.8439 (mtpp) REVERT: E 447 ILE cc_start: 0.8633 (tt) cc_final: 0.8418 (tt) REVERT: E 453 GLU cc_start: 0.8454 (pp20) cc_final: 0.7933 (pp20) REVERT: E 457 ASN cc_start: 0.9099 (m110) cc_final: 0.8688 (m-40) REVERT: E 474 TYR cc_start: 0.7435 (t80) cc_final: 0.7147 (t80) REVERT: E 509 LEU cc_start: 0.8556 (mm) cc_final: 0.8221 (mt) REVERT: E 515 MET cc_start: 0.7228 (pp-130) cc_final: 0.6524 (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: 0.8555 (mtpp) REVERT: G 458 GLN cc_start: 0.8563 (pt0) cc_final: 0.8141 (pt0) REVERT: G 509 LEU cc_start: 0.8288 (mm) cc_final: 0.7969 (mt) REVERT: G 515 MET cc_start: 0.7146 (pp-130) cc_final: 0.6776 (pp-130) REVERT: H 439 TRP cc_start: 0.8004 (t60) cc_final: 0.7533 (t60) REVERT: H 457 ASN cc_start: 0.9074 (m110) cc_final: 0.8312 (t0) REVERT: H 458 GLN cc_start: 0.8873 (pt0) cc_final: 0.8405 (pt0) REVERT: H 509 LEU cc_start: 0.8612 (mm) cc_final: 0.8322 (mt) REVERT: H 515 MET cc_start: 0.7211 (pp-130) cc_final: 0.6430 (pp-130) REVERT: I 439 TRP cc_start: 0.7832 (t60) cc_final: 0.7188 (t60) REVERT: I 443 LYS cc_start: 0.8784 (mmtt) cc_final: 0.8459 (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: 0.7556 (t80) REVERT: I 515 MET cc_start: 0.7162 (pp-130) cc_final: 0.6420 (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: 0.8314 (t0) REVERT: J 458 GLN cc_start: 0.8737 (pt0) cc_final: 0.8236 (pt0) REVERT: J 515 MET cc_start: 0.7266 (pp-130) cc_final: 0.6822 (pp-130) outliers start: 10 outliers final: 0 residues processed: 399 average time/residue: 0.0888 time to fit residues: 46.7118 Evaluate side-chains 336 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 489 GLN ** 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 437 GLN B 489 GLN ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 GLN ** C 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 489 GLN ** G 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 489 GLN ** H 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 489 GLN I 512 ASN I 514 GLN 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.127791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.113453 restraints weight = 13486.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.117069 restraints weight = 7397.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.119646 restraints weight = 4682.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.121439 restraints weight = 3195.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.122730 restraints weight = 2305.428| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6930 Z= 0.169 Angle : 0.826 9.323 9300 Z= 0.403 Chirality : 0.044 0.124 1100 Planarity : 0.003 0.015 1190 Dihedral : 6.338 16.442 900 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.92 % Allowed : 17.09 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.89 (0.21), residues: 840 helix: -4.36 (0.11), residues: 590 sheet: None (None), residues: 0 loop : -1.97 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 488 TYR 0.006 0.001 TYR B 474 PHE 0.008 0.003 PHE E 501 TRP 0.007 0.001 TRP H 439 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 6930) covalent geometry : angle 0.82593 ( 9300) hydrogen bonds : bond 0.04661 ( 220) hydrogen bonds : angle 6.36540 ( 600) *********************** 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 384 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 353 time to evaluate : 0.288 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: F 439 TRP cc_start: 0.7919 (t60) cc_final: 0.7318 (t60) REVERT: F 444 ARG cc_start: 0.8971 (ttt180) cc_final: 0.8695 (ttt180) REVERT: F 457 ASN cc_start: 0.9260 (m110) cc_final: 0.8964 (m-40) REVERT: F 469 ILE cc_start: 0.8924 (tp) cc_final: 0.8579 (tt) REVERT: F 470 MET cc_start: 0.7264 (mtp) cc_final: 0.6569 (mtt) REVERT: F 474 TYR cc_start: 0.7216 (t80) cc_final: 0.6759 (t80) REVERT: F 515 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.6422 (pp-130) REVERT: A 437 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.6632 (mt0) REVERT: A 441 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7167 (tm-30) REVERT: A 457 ASN cc_start: 0.9146 (m110) cc_final: 0.8894 (m-40) REVERT: A 461 ASP cc_start: 0.8819 (t70) cc_final: 0.8580 (t70) REVERT: A 473 ASP cc_start: 0.8442 (p0) cc_final: 0.8034 (p0) REVERT: A 482 THR cc_start: 0.8108 (t) cc_final: 0.7838 (t) REVERT: B 440 ILE cc_start: 0.9327 (OUTLIER) cc_final: 0.8960 (mt) REVERT: B 458 GLN cc_start: 0.8692 (pt0) cc_final: 0.8263 (pt0) REVERT: B 461 ASP cc_start: 0.8521 (t70) cc_final: 0.8255 (t70) REVERT: B 469 ILE cc_start: 0.8987 (tp) cc_final: 0.8626 (tt) REVERT: B 474 TYR cc_start: 0.7535 (t80) cc_final: 0.7285 (t80) REVERT: B 482 THR cc_start: 0.8119 (t) cc_final: 0.7732 (t) REVERT: B 500 GLU cc_start: 0.6140 (mp0) cc_final: 0.5882 (mp0) REVERT: B 505 ILE cc_start: 0.8966 (tt) cc_final: 0.8764 (tt) REVERT: B 515 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.6735 (pp-130) REVERT: C 440 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.9066 (mt) REVERT: C 443 LYS cc_start: 0.8823 (mmtt) cc_final: 0.8526 (tptp) REVERT: C 457 ASN cc_start: 0.9183 (m110) cc_final: 0.8884 (m-40) REVERT: C 458 GLN cc_start: 0.8514 (pt0) cc_final: 0.7935 (pt0) REVERT: C 469 ILE cc_start: 0.8995 (tp) cc_final: 0.8687 (tt) REVERT: C 505 ILE cc_start: 0.8992 (tt) cc_final: 0.8724 (tt) REVERT: D 443 LYS cc_start: 0.8862 (mmtt) cc_final: 0.8202 (mmtt) REVERT: D 457 ASN cc_start: 0.9365 (m110) cc_final: 0.8986 (m-40) REVERT: D 458 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7897 (pt0) REVERT: D 469 ILE cc_start: 0.8998 (tp) cc_final: 0.8753 (tt) REVERT: D 473 ASP cc_start: 0.8330 (p0) cc_final: 0.7960 (p0) REVERT: D 474 TYR cc_start: 0.7385 (t80) cc_final: 0.6748 (t80) REVERT: D 515 MET cc_start: 0.6940 (OUTLIER) cc_final: 0.6651 (pp-130) REVERT: E 439 TRP cc_start: 0.7986 (t60) cc_final: 0.7484 (t60) REVERT: E 443 LYS cc_start: 0.8810 (mmtt) cc_final: 0.8536 (mtpp) REVERT: E 458 GLN cc_start: 0.8338 (pt0) cc_final: 0.7789 (pt0) REVERT: E 474 TYR cc_start: 0.7409 (t80) cc_final: 0.7126 (t80) REVERT: E 482 THR cc_start: 0.8305 (t) cc_final: 0.7931 (t) REVERT: E 500 GLU cc_start: 0.7096 (mp0) cc_final: 0.6840 (mp0) REVERT: E 515 MET cc_start: 0.6855 (OUTLIER) cc_final: 0.6508 (pp-130) REVERT: G 458 GLN cc_start: 0.8627 (pt0) cc_final: 0.8297 (pt0) REVERT: H 482 THR cc_start: 0.8561 (t) cc_final: 0.8205 (t) REVERT: H 515 MET cc_start: 0.7004 (OUTLIER) cc_final: 0.6463 (pp-130) REVERT: I 443 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8426 (tptp) REVERT: I 474 TYR cc_start: 0.7530 (t80) cc_final: 0.7290 (t80) REVERT: I 482 THR cc_start: 0.8271 (t) cc_final: 0.7897 (t) REVERT: I 500 GLU cc_start: 0.6522 (mp0) cc_final: 0.6167 (mp0) REVERT: I 505 ILE cc_start: 0.8894 (tt) cc_final: 0.8657 (tt) REVERT: J 439 TRP cc_start: 0.7829 (t60) cc_final: 0.7368 (t60) REVERT: J 441 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7538 (mp10) REVERT: J 473 ASP cc_start: 0.8440 (p0) cc_final: 0.8093 (p0) REVERT: J 515 MET cc_start: 0.6919 (OUTLIER) cc_final: 0.6525 (pp-130) outliers start: 31 outliers final: 3 residues processed: 357 average time/residue: 0.0973 time to fit residues: 44.6911 Evaluate side-chains 341 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 326 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 B residue 440 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 458 GLN Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain E residue 515 MET Chi-restraints excluded: chain H residue 515 MET Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain J residue 515 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 18 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 27 optimal weight: 0.0970 chunk 30 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 457 ASN ** F 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 GLN B 489 GLN ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 GLN ** C 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 450 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 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 ASN G 514 GLN H 512 ASN H 514 GLN I 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.128084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.113844 restraints weight = 13355.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.117387 restraints weight = 7397.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.119864 restraints weight = 4694.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.121754 restraints weight = 3221.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.123050 restraints weight = 2314.484| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 6930 Z= 0.156 Angle : 0.818 10.162 9300 Z= 0.384 Chirality : 0.044 0.125 1100 Planarity : 0.002 0.018 1190 Dihedral : 5.936 16.221 900 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 5.06 % Allowed : 18.99 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.34 (0.21), residues: 840 helix: -3.90 (0.13), residues: 590 sheet: None (None), residues: 0 loop : -1.87 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 488 TYR 0.004 0.001 TYR F 474 PHE 0.011 0.003 PHE A 501 TRP 0.010 0.002 TRP G 439 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 6930) covalent geometry : angle 0.81774 ( 9300) hydrogen bonds : bond 0.04133 ( 220) hydrogen bonds : angle 5.96098 ( 600) *********************** 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 375 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 335 time to evaluate : 0.330 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 444 ARG cc_start: 0.8973 (ttt180) cc_final: 0.8635 (ttt180) REVERT: F 500 GLU cc_start: 0.6630 (mp0) cc_final: 0.6379 (mp0) REVERT: F 515 MET cc_start: 0.6772 (OUTLIER) cc_final: 0.6448 (pp-130) REVERT: A 437 GLN cc_start: 0.7051 (OUTLIER) cc_final: 0.6605 (mt0) REVERT: A 441 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7175 (tm-30) REVERT: A 457 ASN cc_start: 0.9153 (m110) cc_final: 0.8946 (m-40) REVERT: A 466 ARG cc_start: 0.8381 (mpp-170) cc_final: 0.8150 (mtm-85) REVERT: A 473 ASP cc_start: 0.8353 (p0) cc_final: 0.7924 (p0) REVERT: A 482 THR cc_start: 0.8122 (t) cc_final: 0.7758 (t) REVERT: B 458 GLN cc_start: 0.8765 (pt0) cc_final: 0.8335 (pt0) REVERT: B 469 ILE cc_start: 0.9022 (tp) cc_final: 0.8662 (tt) REVERT: B 482 THR cc_start: 0.8160 (t) cc_final: 0.7786 (t) REVERT: B 505 ILE cc_start: 0.8952 (tt) cc_final: 0.8697 (tt) REVERT: B 515 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6627 (pp-130) REVERT: C 440 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.9097 (mt) REVERT: C 443 LYS cc_start: 0.8715 (mmtt) cc_final: 0.8469 (mtpp) REVERT: C 469 ILE cc_start: 0.8956 (tp) cc_final: 0.8688 (tt) REVERT: C 505 ILE cc_start: 0.8950 (tt) cc_final: 0.8681 (tt) REVERT: D 458 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7449 (pt0) REVERT: D 469 ILE cc_start: 0.8931 (tp) cc_final: 0.8633 (tt) REVERT: D 473 ASP cc_start: 0.8350 (p0) cc_final: 0.7947 (p0) REVERT: D 507 GLN cc_start: 0.7528 (pm20) cc_final: 0.7253 (pm20) REVERT: D 515 MET cc_start: 0.6844 (OUTLIER) cc_final: 0.6324 (pp-130) REVERT: E 439 TRP cc_start: 0.7911 (t60) cc_final: 0.7319 (t60) REVERT: E 443 LYS cc_start: 0.8726 (mmtt) cc_final: 0.8391 (mtpp) REVERT: E 450 GLN cc_start: 0.8513 (tm-30) cc_final: 0.8141 (tm-30) REVERT: E 451 MET cc_start: 0.8213 (tpp) cc_final: 0.7925 (tpt) REVERT: E 500 GLU cc_start: 0.7178 (mp0) cc_final: 0.6868 (mp0) REVERT: E 515 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6465 (pp-130) REVERT: G 439 TRP cc_start: 0.8041 (t60) cc_final: 0.7699 (t60) REVERT: G 450 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8057 (tm-30) REVERT: G 458 GLN cc_start: 0.8711 (pt0) cc_final: 0.8289 (pt0) REVERT: H 450 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8324 (tm-30) REVERT: H 451 MET cc_start: 0.8099 (tpt) cc_final: 0.7822 (tpt) REVERT: H 470 MET cc_start: 0.7706 (mtp) cc_final: 0.6752 (mtp) REVERT: H 500 GLU cc_start: 0.6587 (mp0) cc_final: 0.6311 (mp0) REVERT: H 515 MET cc_start: 0.7099 (OUTLIER) cc_final: 0.6528 (pp-130) REVERT: I 450 GLN cc_start: 0.8703 (tm-30) cc_final: 0.8018 (tm-30) REVERT: I 451 MET cc_start: 0.8128 (tpt) cc_final: 0.7732 (tpt) REVERT: I 457 ASN cc_start: 0.8919 (m-40) cc_final: 0.8124 (t0) REVERT: I 482 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.8046 (t) REVERT: I 500 GLU cc_start: 0.6501 (mp0) cc_final: 0.6136 (mp0) REVERT: J 441 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7902 (mp10) REVERT: J 457 ASN cc_start: 0.8864 (m-40) cc_final: 0.8088 (t0) REVERT: J 473 ASP cc_start: 0.8491 (p0) cc_final: 0.8092 (p0) REVERT: J 500 GLU cc_start: 0.6102 (mp0) cc_final: 0.5840 (mp0) REVERT: J 515 MET cc_start: 0.6905 (OUTLIER) cc_final: 0.6627 (pp-130) outliers start: 40 outliers final: 19 residues processed: 345 average time/residue: 0.0895 time to fit residues: 40.1355 Evaluate side-chains 353 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 322 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 504 VAL 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 491 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 509 LEU 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 491 LEU Chi-restraints excluded: chain E residue 515 MET Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain H residue 491 LEU Chi-restraints excluded: chain H residue 515 MET Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 509 LEU 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 2 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 71 optimal weight: 0.0980 chunk 78 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 41 optimal weight: 30.0000 chunk 4 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- 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 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 GLN ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 GLN ** C 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 GLN ** D 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 489 GLN ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 438 GLN ** G 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.131197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.116483 restraints weight = 13350.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.120164 restraints weight = 7346.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.122757 restraints weight = 4619.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.124611 restraints weight = 3145.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.125815 restraints weight = 2268.136| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6930 Z= 0.132 Angle : 0.794 10.801 9300 Z= 0.365 Chirality : 0.043 0.126 1100 Planarity : 0.002 0.024 1190 Dihedral : 5.622 14.175 900 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 5.44 % Allowed : 19.37 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.77 (0.23), residues: 840 helix: -3.41 (0.15), residues: 590 sheet: None (None), residues: 0 loop : -1.84 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 488 TYR 0.007 0.001 TYR B 474 PHE 0.010 0.003 PHE A 501 TRP 0.016 0.002 TRP H 439 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 6930) covalent geometry : angle 0.79412 ( 9300) hydrogen bonds : bond 0.03861 ( 220) hydrogen bonds : angle 5.71563 ( 600) *********************** 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 391 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 348 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 458 GLN cc_start: 0.8659 (pt0) cc_final: 0.7449 (pt0) REVERT: F 500 GLU cc_start: 0.6267 (mp0) cc_final: 0.5976 (mp0) REVERT: F 515 MET cc_start: 0.6478 (OUTLIER) cc_final: 0.6100 (pp-130) REVERT: A 437 GLN cc_start: 0.7314 (mt0) cc_final: 0.6626 (mt0) REVERT: A 439 TRP cc_start: 0.8158 (t60) cc_final: 0.7945 (t60) REVERT: A 441 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7059 (tm-30) REVERT: A 451 MET cc_start: 0.8141 (tmm) cc_final: 0.7899 (tmm) REVERT: A 457 ASN cc_start: 0.9144 (m110) cc_final: 0.8900 (m-40) REVERT: A 461 ASP cc_start: 0.8879 (t70) cc_final: 0.8624 (t70) REVERT: A 473 ASP cc_start: 0.8326 (p0) cc_final: 0.7716 (p0) REVERT: A 474 TYR cc_start: 0.7572 (t80) cc_final: 0.7246 (t80) REVERT: A 482 THR cc_start: 0.8042 (t) cc_final: 0.7667 (t) REVERT: B 440 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8826 (mt) REVERT: B 443 LYS cc_start: 0.8925 (mmtp) cc_final: 0.8455 (mtpp) REVERT: B 457 ASN cc_start: 0.9137 (m-40) cc_final: 0.8846 (m-40) REVERT: B 469 ILE cc_start: 0.8983 (tp) cc_final: 0.8612 (tt) REVERT: B 482 THR cc_start: 0.8156 (t) cc_final: 0.7801 (t) REVERT: B 505 ILE cc_start: 0.8852 (tt) cc_final: 0.8616 (tt) REVERT: B 515 MET cc_start: 0.7166 (OUTLIER) cc_final: 0.6582 (pp-130) REVERT: B 517 LEU cc_start: 0.7713 (mt) cc_final: 0.7456 (mp) REVERT: C 443 LYS cc_start: 0.8700 (mmtt) cc_final: 0.8410 (mmmt) REVERT: C 450 GLN cc_start: 0.8579 (tm-30) cc_final: 0.7851 (tm-30) REVERT: C 461 ASP cc_start: 0.8799 (t70) cc_final: 0.8483 (t0) REVERT: C 469 ILE cc_start: 0.8863 (tp) cc_final: 0.8607 (tt) REVERT: C 505 ILE cc_start: 0.8869 (tt) cc_final: 0.8597 (tt) REVERT: D 437 GLN cc_start: 0.7429 (mt0) cc_final: 0.7104 (mt0) REVERT: D 458 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7539 (pt0) REVERT: D 469 ILE cc_start: 0.8899 (tp) cc_final: 0.8569 (tt) REVERT: D 473 ASP cc_start: 0.8349 (p0) cc_final: 0.7993 (p0) REVERT: D 515 MET cc_start: 0.6773 (OUTLIER) cc_final: 0.6363 (pp-130) REVERT: E 439 TRP cc_start: 0.7940 (t60) cc_final: 0.7363 (t60) REVERT: E 443 LYS cc_start: 0.8789 (mmtt) cc_final: 0.8477 (mtpp) REVERT: E 444 ARG cc_start: 0.8784 (ttt180) cc_final: 0.8339 (ttt180) REVERT: E 450 GLN cc_start: 0.8515 (tm-30) cc_final: 0.8130 (tm-30) REVERT: E 451 MET cc_start: 0.8211 (tpp) cc_final: 0.7700 (tpt) REVERT: E 472 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.5864 (pp20) REVERT: E 500 GLU cc_start: 0.7103 (mp0) cc_final: 0.6824 (mp0) REVERT: E 515 MET cc_start: 0.6895 (OUTLIER) cc_final: 0.6463 (pp-130) REVERT: G 450 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8033 (tm-30) REVERT: G 458 GLN cc_start: 0.8691 (pt0) cc_final: 0.8349 (pt0) REVERT: G 500 GLU cc_start: 0.6533 (mp0) cc_final: 0.6323 (mp0) REVERT: H 443 LYS cc_start: 0.8687 (mtpp) cc_final: 0.7809 (mtpp) REVERT: H 450 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8328 (tm-30) REVERT: H 451 MET cc_start: 0.8333 (tpt) cc_final: 0.7860 (tpt) REVERT: H 457 ASN cc_start: 0.8799 (m-40) cc_final: 0.7804 (t0) REVERT: H 470 MET cc_start: 0.7390 (mtp) cc_final: 0.6567 (mtp) REVERT: H 500 GLU cc_start: 0.6545 (mp0) cc_final: 0.6246 (mp0) REVERT: H 515 MET cc_start: 0.6964 (OUTLIER) cc_final: 0.6481 (pp-130) REVERT: I 443 LYS cc_start: 0.8325 (mtpp) cc_final: 0.8116 (mtpp) REVERT: I 450 GLN cc_start: 0.8616 (tm-30) cc_final: 0.7769 (tm-30) REVERT: I 451 MET cc_start: 0.8249 (tpt) cc_final: 0.7803 (tpt) REVERT: I 457 ASN cc_start: 0.8874 (m-40) cc_final: 0.8041 (t0) REVERT: I 482 THR cc_start: 0.8394 (OUTLIER) cc_final: 0.8045 (t) REVERT: I 500 GLU cc_start: 0.6464 (mp0) cc_final: 0.6136 (mp0) REVERT: J 439 TRP cc_start: 0.8506 (t60) cc_final: 0.8296 (t60) REVERT: J 441 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7940 (mp10) REVERT: J 457 ASN cc_start: 0.8853 (m-40) cc_final: 0.8286 (t0) REVERT: J 470 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6210 (mtt) REVERT: J 473 ASP cc_start: 0.8396 (p0) cc_final: 0.7931 (p0) REVERT: J 500 GLU cc_start: 0.6201 (mp0) cc_final: 0.5882 (mp0) REVERT: J 515 MET cc_start: 0.6804 (OUTLIER) cc_final: 0.6545 (pp-130) outliers start: 43 outliers final: 23 residues processed: 359 average time/residue: 0.0948 time to fit residues: 44.1147 Evaluate side-chains 361 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 325 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 515 MET Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 489 GLN Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain C residue 489 GLN Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 509 LEU 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 472 GLU Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 509 LEU Chi-restraints excluded: chain E residue 515 MET Chi-restraints excluded: chain G residue 448 VAL Chi-restraints excluded: chain H residue 460 LEU Chi-restraints excluded: chain H residue 491 LEU Chi-restraints excluded: chain H residue 515 MET Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain J residue 453 GLU Chi-restraints excluded: chain J residue 470 MET Chi-restraints excluded: chain J residue 509 LEU Chi-restraints excluded: chain J residue 515 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 1 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 ** 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 489 GLN ** D 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 457 ASN ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.130020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.115308 restraints weight = 13576.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.118986 restraints weight = 7426.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.121427 restraints weight = 4659.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.123333 restraints weight = 3238.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.124674 restraints weight = 2325.930| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6930 Z= 0.153 Angle : 0.853 12.335 9300 Z= 0.380 Chirality : 0.045 0.153 1100 Planarity : 0.002 0.017 1190 Dihedral : 5.581 14.122 900 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 6.58 % Allowed : 21.52 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.40 (0.24), residues: 840 helix: -3.09 (0.16), residues: 590 sheet: None (None), residues: 0 loop : -1.83 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 466 TYR 0.007 0.001 TYR F 474 PHE 0.011 0.004 PHE F 501 TRP 0.016 0.002 TRP D 439 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 6930) covalent geometry : angle 0.85343 ( 9300) hydrogen bonds : bond 0.03689 ( 220) hydrogen bonds : angle 5.64628 ( 600) *********************** 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 386 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 334 time to evaluate : 0.278 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: 0.8335 (t60) cc_final: 0.8127 (t60) REVERT: F 441 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7838 (pm20) REVERT: F 458 GLN cc_start: 0.8602 (pt0) cc_final: 0.7300 (pt0) REVERT: F 470 MET cc_start: 0.6830 (mtt) cc_final: 0.6214 (mtt) REVERT: F 500 GLU cc_start: 0.6305 (mp0) cc_final: 0.6029 (mp0) REVERT: F 515 MET cc_start: 0.6582 (OUTLIER) cc_final: 0.6260 (pp-130) REVERT: A 437 GLN cc_start: 0.7683 (mt0) cc_final: 0.6693 (mt0) REVERT: A 441 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7033 (tm-30) REVERT: A 450 GLN cc_start: 0.8708 (tm-30) cc_final: 0.8444 (tm-30) REVERT: A 451 MET cc_start: 0.8096 (tmm) cc_final: 0.7808 (tmm) REVERT: A 458 GLN cc_start: 0.8371 (pt0) cc_final: 0.7757 (pt0) REVERT: A 482 THR cc_start: 0.8133 (t) cc_final: 0.7778 (t) REVERT: B 443 LYS cc_start: 0.8930 (mmtp) cc_final: 0.8439 (mtpp) REVERT: B 458 GLN cc_start: 0.8702 (pt0) cc_final: 0.8021 (pt0) REVERT: B 469 ILE cc_start: 0.9004 (tp) cc_final: 0.8654 (tt) REVERT: B 482 THR cc_start: 0.8178 (t) cc_final: 0.7729 (t) REVERT: B 515 MET cc_start: 0.7202 (OUTLIER) cc_final: 0.6586 (pp-130) REVERT: B 517 LEU cc_start: 0.7756 (mt) cc_final: 0.7492 (mp) REVERT: C 450 GLN cc_start: 0.8613 (tm-30) cc_final: 0.7911 (tm-30) REVERT: C 458 GLN cc_start: 0.8623 (pt0) cc_final: 0.8312 (pt0) REVERT: C 466 ARG cc_start: 0.8341 (mtm-85) cc_final: 0.8049 (mtm-85) REVERT: C 469 ILE cc_start: 0.8891 (tp) cc_final: 0.8634 (tt) REVERT: D 458 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7489 (pt0) REVERT: D 469 ILE cc_start: 0.8918 (tp) cc_final: 0.8580 (tt) REVERT: D 473 ASP cc_start: 0.8467 (p0) cc_final: 0.8182 (p0) REVERT: D 515 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6498 (pp-130) REVERT: D 517 LEU cc_start: 0.7519 (mp) cc_final: 0.7261 (mp) REVERT: E 439 TRP cc_start: 0.7958 (t60) cc_final: 0.7562 (t60) REVERT: E 443 LYS cc_start: 0.8832 (mmtt) cc_final: 0.8492 (mtpp) REVERT: E 444 ARG cc_start: 0.8830 (ttt180) cc_final: 0.8441 (ttt180) REVERT: E 450 GLN cc_start: 0.8602 (tm-30) cc_final: 0.7427 (tm-30) REVERT: E 451 MET cc_start: 0.8246 (tpp) cc_final: 0.7891 (tpt) REVERT: E 472 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.5993 (pp20) REVERT: E 500 GLU cc_start: 0.7094 (mp0) cc_final: 0.6811 (mp0) REVERT: E 515 MET cc_start: 0.7009 (OUTLIER) cc_final: 0.6573 (pp-130) REVERT: G 450 GLN cc_start: 0.8795 (tm-30) cc_final: 0.7995 (tm-30) REVERT: G 458 GLN cc_start: 0.8673 (pt0) cc_final: 0.8359 (pt0) REVERT: H 450 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8309 (tm-30) REVERT: H 451 MET cc_start: 0.8404 (tpt) cc_final: 0.7923 (tpt) REVERT: H 457 ASN cc_start: 0.8869 (m-40) cc_final: 0.7952 (t0) REVERT: H 458 GLN cc_start: 0.8865 (pt0) cc_final: 0.8346 (pt0) REVERT: H 470 MET cc_start: 0.7590 (mtp) cc_final: 0.6579 (mtp) REVERT: H 500 GLU cc_start: 0.6640 (mp0) cc_final: 0.6351 (mp0) REVERT: H 515 MET cc_start: 0.6972 (OUTLIER) cc_final: 0.6250 (pp-130) REVERT: I 450 GLN cc_start: 0.8652 (tm-30) cc_final: 0.7799 (tm-30) REVERT: I 451 MET cc_start: 0.8207 (tpt) cc_final: 0.7688 (tpt) REVERT: I 457 ASN cc_start: 0.8785 (m-40) cc_final: 0.8105 (t0) REVERT: I 482 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8167 (t) REVERT: I 500 GLU cc_start: 0.6369 (mp0) cc_final: 0.6005 (mp0) REVERT: J 441 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7954 (mp10) REVERT: J 451 MET cc_start: 0.7986 (tmm) cc_final: 0.7560 (ttt) REVERT: J 457 ASN cc_start: 0.8755 (m-40) cc_final: 0.8325 (t0) REVERT: J 470 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6299 (mtt) REVERT: J 473 ASP cc_start: 0.8489 (p0) cc_final: 0.8068 (p0) REVERT: J 500 GLU cc_start: 0.6331 (mp0) cc_final: 0.5985 (mp0) REVERT: J 515 MET cc_start: 0.6758 (OUTLIER) cc_final: 0.6400 (pp-130) outliers start: 52 outliers final: 35 residues processed: 345 average time/residue: 0.0911 time to fit residues: 41.2329 Evaluate side-chains 370 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 322 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 441 GLN 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 F residue 515 MET Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 489 GLN Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 489 GLN Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain D residue 458 GLN Chi-restraints excluded: chain D residue 489 GLN Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain E residue 453 GLU Chi-restraints excluded: chain E residue 458 GLN Chi-restraints excluded: chain E residue 472 GLU Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 509 LEU Chi-restraints excluded: chain E residue 515 MET Chi-restraints excluded: chain G residue 448 VAL Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 491 LEU Chi-restraints excluded: chain G residue 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 504 VAL Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain J residue 453 GLU Chi-restraints excluded: chain J residue 470 MET Chi-restraints excluded: chain J residue 509 LEU Chi-restraints excluded: chain J residue 515 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 24 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 26 optimal weight: 0.0670 chunk 21 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 overall best weight: 2.3724 ------------------------------------------------------------------------------- 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 437 GLN 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 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 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN D 457 ASN ** D 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 438 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.131302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.116832 restraints weight = 13439.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.120585 restraints weight = 7224.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.123206 restraints weight = 4496.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.124986 restraints weight = 3041.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.126235 restraints weight = 2191.159| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6930 Z= 0.131 Angle : 0.853 12.201 9300 Z= 0.381 Chirality : 0.044 0.146 1100 Planarity : 0.003 0.022 1190 Dihedral : 5.410 14.720 900 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 7.47 % Allowed : 20.13 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.46 (0.23), residues: 840 helix: -2.86 (0.17), residues: 610 sheet: None (None), residues: 0 loop : -2.55 (0.33), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 466 TYR 0.008 0.001 TYR F 474 PHE 0.011 0.003 PHE A 501 TRP 0.014 0.002 TRP D 439 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 6930) covalent geometry : angle 0.85275 ( 9300) hydrogen bonds : bond 0.03722 ( 220) hydrogen bonds : angle 5.52349 ( 600) *********************** 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 398 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 339 time to evaluate : 0.292 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 458 GLN cc_start: 0.8631 (pt0) cc_final: 0.7537 (pt0) REVERT: F 470 MET cc_start: 0.6787 (mtt) cc_final: 0.6362 (mtt) REVERT: F 500 GLU cc_start: 0.6290 (mp0) cc_final: 0.6000 (mp0) REVERT: F 515 MET cc_start: 0.6515 (OUTLIER) cc_final: 0.6224 (pp-130) REVERT: A 437 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.6959 (mt0) REVERT: A 441 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.6978 (tm-30) REVERT: A 450 GLN cc_start: 0.8745 (tm-30) cc_final: 0.8483 (tm-30) REVERT: A 451 MET cc_start: 0.7929 (tmm) cc_final: 0.7664 (tmm) REVERT: A 473 ASP cc_start: 0.8405 (p0) cc_final: 0.7974 (p0) REVERT: A 482 THR cc_start: 0.8114 (t) cc_final: 0.7768 (t) REVERT: B 437 GLN cc_start: 0.7693 (mt0) cc_final: 0.7338 (mt0) REVERT: B 443 LYS cc_start: 0.8888 (mmtp) cc_final: 0.8422 (mtpp) REVERT: B 450 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8116 (tm-30) REVERT: B 458 GLN cc_start: 0.8734 (pt0) cc_final: 0.8084 (pt0) REVERT: B 469 ILE cc_start: 0.8974 (tp) cc_final: 0.8635 (tt) REVERT: B 482 THR cc_start: 0.8205 (t) cc_final: 0.7823 (t) REVERT: B 515 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.6531 (pp-130) REVERT: B 517 LEU cc_start: 0.7798 (mt) cc_final: 0.7559 (mp) REVERT: C 450 GLN cc_start: 0.8716 (tm-30) cc_final: 0.7750 (tm-30) REVERT: C 500 GLU cc_start: 0.6627 (mp0) cc_final: 0.6387 (mp0) REVERT: D 444 ARG cc_start: 0.8842 (ttt180) cc_final: 0.8628 (ttt180) REVERT: D 458 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7518 (pt0) REVERT: D 469 ILE cc_start: 0.8876 (tp) cc_final: 0.8558 (tt) REVERT: D 473 ASP cc_start: 0.8426 (p0) cc_final: 0.8213 (p0) REVERT: D 515 MET cc_start: 0.6898 (OUTLIER) cc_final: 0.6371 (pp-130) REVERT: D 517 LEU cc_start: 0.7591 (mp) cc_final: 0.7228 (mp) REVERT: E 439 TRP cc_start: 0.7831 (t60) cc_final: 0.7258 (t60) REVERT: E 443 LYS cc_start: 0.8849 (mmtt) cc_final: 0.8503 (mtpp) REVERT: E 450 GLN cc_start: 0.8597 (tm-30) cc_final: 0.7456 (tm-30) REVERT: E 451 MET cc_start: 0.8330 (tpp) cc_final: 0.8128 (tpt) REVERT: E 470 MET cc_start: 0.7402 (mtp) cc_final: 0.6818 (mtp) REVERT: E 472 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.6067 (pp20) REVERT: E 500 GLU cc_start: 0.7003 (mp0) cc_final: 0.6794 (mp0) REVERT: E 515 MET cc_start: 0.6926 (OUTLIER) cc_final: 0.6524 (pp-130) REVERT: G 439 TRP cc_start: 0.8361 (t60) cc_final: 0.7932 (t60) REVERT: G 450 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8026 (tm-30) REVERT: G 458 GLN cc_start: 0.8628 (pt0) cc_final: 0.8269 (pt0) REVERT: G 515 MET cc_start: 0.6039 (pp-130) cc_final: 0.4748 (pp-130) REVERT: H 450 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8292 (tm-30) REVERT: H 451 MET cc_start: 0.8416 (tpt) cc_final: 0.7912 (tpt) REVERT: H 457 ASN cc_start: 0.8838 (m-40) cc_final: 0.8304 (t0) REVERT: H 458 GLN cc_start: 0.8861 (pt0) cc_final: 0.8409 (pt0) REVERT: H 470 MET cc_start: 0.7582 (mtp) cc_final: 0.6675 (mtp) REVERT: H 500 GLU cc_start: 0.6614 (mp0) cc_final: 0.6239 (mp0) REVERT: H 515 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.6233 (pp-130) REVERT: I 450 GLN cc_start: 0.8688 (tm-30) cc_final: 0.7837 (tm-30) REVERT: I 451 MET cc_start: 0.8372 (tpt) cc_final: 0.7833 (tpt) REVERT: I 457 ASN cc_start: 0.8785 (m-40) cc_final: 0.8100 (t0) REVERT: I 473 ASP cc_start: 0.8375 (p0) cc_final: 0.8158 (p0) REVERT: I 482 THR cc_start: 0.8462 (OUTLIER) cc_final: 0.8139 (t) REVERT: I 500 GLU cc_start: 0.6780 (mp0) cc_final: 0.6269 (mp0) REVERT: J 439 TRP cc_start: 0.8298 (t60) cc_final: 0.7755 (t60) REVERT: J 441 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7937 (mp10) REVERT: J 457 ASN cc_start: 0.8807 (m-40) cc_final: 0.8236 (t0) REVERT: J 470 MET cc_start: 0.7073 (OUTLIER) cc_final: 0.6416 (mtt) REVERT: J 472 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6512 (pp20) REVERT: J 473 ASP cc_start: 0.8512 (p0) cc_final: 0.8162 (p0) REVERT: J 500 GLU cc_start: 0.6430 (mp0) cc_final: 0.6108 (mp0) REVERT: J 515 MET cc_start: 0.6817 (OUTLIER) cc_final: 0.6498 (pp-130) outliers start: 59 outliers final: 34 residues processed: 351 average time/residue: 0.0941 time to fit residues: 42.9882 Evaluate side-chains 367 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 319 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 491 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 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 472 GLU Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 509 LEU Chi-restraints excluded: chain E residue 515 MET Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain G residue 504 VAL Chi-restraints excluded: chain H residue 491 LEU Chi-restraints excluded: chain H residue 509 LEU Chi-restraints excluded: chain H residue 515 MET Chi-restraints excluded: chain I residue 453 GLU Chi-restraints excluded: chain I residue 482 THR 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 470 MET Chi-restraints excluded: chain J residue 472 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 Chi-restraints excluded: chain J residue 515 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 19 optimal weight: 20.0000 chunk 3 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 overall best weight: 3.7786 ------------------------------------------------------------------------------- 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 437 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 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN D 489 GLN ** D 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 514 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** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.129884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.115344 restraints weight = 13517.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.119049 restraints weight = 7356.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.121629 restraints weight = 4619.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.123365 restraints weight = 3154.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.124621 restraints weight = 2287.095| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6930 Z= 0.154 Angle : 0.870 11.757 9300 Z= 0.393 Chirality : 0.045 0.142 1100 Planarity : 0.003 0.032 1190 Dihedral : 5.399 14.579 900 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 6.96 % Allowed : 22.78 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.32 (0.24), residues: 840 helix: -2.75 (0.17), residues: 610 sheet: None (None), residues: 0 loop : -2.53 (0.33), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 466 TYR 0.007 0.001 TYR F 474 PHE 0.014 0.004 PHE A 501 TRP 0.026 0.002 TRP F 439 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 6930) covalent geometry : angle 0.86995 ( 9300) hydrogen bonds : bond 0.03637 ( 220) hydrogen bonds : angle 5.52601 ( 600) *********************** 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 386 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 331 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 450 GLN cc_start: 0.8587 (tm-30) cc_final: 0.7804 (tm-30) REVERT: F 451 MET cc_start: 0.7952 (tmm) cc_final: 0.7663 (tmm) REVERT: F 500 GLU cc_start: 0.6373 (mp0) cc_final: 0.6066 (mp0) REVERT: F 512 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7809 (t0) REVERT: F 515 MET cc_start: 0.6683 (OUTLIER) cc_final: 0.6221 (pp-130) REVERT: A 437 GLN cc_start: 0.7733 (mt0) cc_final: 0.6770 (mt0) REVERT: A 439 TRP cc_start: 0.8343 (t60) cc_final: 0.7987 (t60) REVERT: A 441 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7077 (tm-30) REVERT: A 450 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8454 (tm-30) REVERT: A 451 MET cc_start: 0.7853 (tmm) cc_final: 0.7524 (tmm) REVERT: A 458 GLN cc_start: 0.8313 (pt0) cc_final: 0.8031 (pt0) REVERT: A 461 ASP cc_start: 0.9005 (t70) cc_final: 0.8803 (t70) REVERT: A 473 ASP cc_start: 0.8425 (p0) cc_final: 0.7953 (p0) REVERT: A 482 THR cc_start: 0.8160 (t) cc_final: 0.7784 (t) REVERT: A 515 MET cc_start: 0.6488 (pp-130) cc_final: 0.5365 (pp-130) REVERT: B 443 LYS cc_start: 0.8891 (mmtp) cc_final: 0.8403 (mtpp) REVERT: B 450 GLN cc_start: 0.8647 (tm-30) cc_final: 0.7833 (tm-30) REVERT: B 451 MET cc_start: 0.8233 (tmm) cc_final: 0.7832 (tmm) REVERT: B 457 ASN cc_start: 0.8996 (m-40) cc_final: 0.8617 (m-40) REVERT: B 458 GLN cc_start: 0.8780 (pt0) cc_final: 0.8394 (pt0) REVERT: B 461 ASP cc_start: 0.8818 (t70) cc_final: 0.8601 (t0) REVERT: B 469 ILE cc_start: 0.8997 (tp) cc_final: 0.8645 (tt) REVERT: B 482 THR cc_start: 0.7808 (t) cc_final: 0.7416 (t) REVERT: B 515 MET cc_start: 0.6980 (OUTLIER) cc_final: 0.6408 (pp-130) REVERT: C 450 GLN cc_start: 0.8738 (tm-30) cc_final: 0.7779 (tm-30) REVERT: C 500 GLU cc_start: 0.6767 (mp0) cc_final: 0.6485 (mp0) REVERT: D 458 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7525 (pt0) REVERT: D 469 ILE cc_start: 0.8898 (tp) cc_final: 0.8584 (tt) REVERT: D 473 ASP cc_start: 0.8501 (p0) cc_final: 0.8254 (p0) REVERT: D 515 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6342 (pp-130) REVERT: E 439 TRP cc_start: 0.7861 (t60) cc_final: 0.7300 (t60) REVERT: E 443 LYS cc_start: 0.8833 (mmtt) cc_final: 0.8469 (mtpp) REVERT: E 450 GLN cc_start: 0.8693 (tm-30) cc_final: 0.7640 (tm-30) REVERT: E 451 MET cc_start: 0.8359 (tpp) cc_final: 0.7860 (tpt) REVERT: E 492 ASP cc_start: 0.8362 (p0) cc_final: 0.8014 (m-30) REVERT: E 500 GLU cc_start: 0.7088 (mp0) cc_final: 0.6881 (mp0) REVERT: G 439 TRP cc_start: 0.8324 (t60) cc_final: 0.7871 (t60) REVERT: G 450 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8099 (tm-30) REVERT: G 458 GLN cc_start: 0.8600 (pt0) cc_final: 0.8113 (pt0) REVERT: G 515 MET cc_start: 0.6139 (pp-130) cc_final: 0.5317 (pp-130) REVERT: H 450 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8373 (tm-30) REVERT: H 451 MET cc_start: 0.8405 (tpt) cc_final: 0.7880 (tpt) REVERT: H 457 ASN cc_start: 0.8899 (m-40) cc_final: 0.8139 (t0) REVERT: H 458 GLN cc_start: 0.8918 (pt0) cc_final: 0.8410 (pt0) REVERT: H 470 MET cc_start: 0.7549 (mtp) cc_final: 0.6514 (mtp) REVERT: H 500 GLU cc_start: 0.6702 (mp0) cc_final: 0.6303 (mp0) REVERT: H 515 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.6157 (pp-130) REVERT: I 450 GLN cc_start: 0.8738 (tm-30) cc_final: 0.7886 (tm-30) REVERT: I 451 MET cc_start: 0.8336 (tpt) cc_final: 0.7755 (tpt) REVERT: I 457 ASN cc_start: 0.8836 (m-40) cc_final: 0.8166 (t0) REVERT: I 458 GLN cc_start: 0.8848 (pt0) cc_final: 0.8256 (pt0) REVERT: I 473 ASP cc_start: 0.8363 (p0) cc_final: 0.8138 (p0) REVERT: I 482 THR cc_start: 0.8450 (OUTLIER) cc_final: 0.8188 (t) REVERT: I 500 GLU cc_start: 0.6863 (mp0) cc_final: 0.6360 (mp0) REVERT: J 439 TRP cc_start: 0.8316 (t60) cc_final: 0.8063 (t60) REVERT: J 441 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7822 (mp10) REVERT: J 457 ASN cc_start: 0.8742 (m-40) cc_final: 0.8306 (t0) REVERT: J 470 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.6763 (mtt) REVERT: J 472 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6599 (pp20) REVERT: J 473 ASP cc_start: 0.8562 (p0) cc_final: 0.8248 (p0) REVERT: J 500 GLU cc_start: 0.6482 (mp0) cc_final: 0.6157 (mp0) REVERT: J 515 MET cc_start: 0.6929 (OUTLIER) cc_final: 0.6709 (pp-130) outliers start: 55 outliers final: 34 residues processed: 343 average time/residue: 0.0914 time to fit residues: 40.9955 Evaluate side-chains 366 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 320 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 512 ASN Chi-restraints excluded: chain F residue 515 MET Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain 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 482 THR 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 489 GLN Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 515 MET Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 509 LEU Chi-restraints excluded: chain G residue 460 LEU Chi-restraints excluded: chain G residue 482 THR Chi-restraints excluded: chain H residue 482 THR Chi-restraints excluded: chain H residue 509 LEU Chi-restraints excluded: chain H residue 515 MET Chi-restraints excluded: chain I residue 453 GLU Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain I residue 509 LEU Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain J residue 447 ILE Chi-restraints excluded: chain J residue 453 GLU Chi-restraints excluded: chain J residue 470 MET Chi-restraints excluded: chain J residue 472 GLU Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 495 ASP Chi-restraints excluded: chain J residue 504 VAL Chi-restraints excluded: chain J residue 515 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 35 optimal weight: 0.1980 chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- 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 458 GLN ** A 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 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** ** D 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.131626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.116994 restraints weight = 13538.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.120761 restraints weight = 7328.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.123376 restraints weight = 4568.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.125187 restraints weight = 3090.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.126472 restraints weight = 2220.065| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6930 Z= 0.149 Angle : 0.908 11.415 9300 Z= 0.408 Chirality : 0.045 0.160 1100 Planarity : 0.003 0.022 1190 Dihedral : 5.374 14.993 900 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 6.84 % Allowed : 23.04 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.77 (0.26), residues: 840 helix: -2.54 (0.19), residues: 590 sheet: None (None), residues: 0 loop : -1.83 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 466 TYR 0.009 0.001 TYR F 474 PHE 0.012 0.003 PHE A 501 TRP 0.026 0.002 TRP F 439 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 6930) covalent geometry : angle 0.90766 ( 9300) hydrogen bonds : bond 0.03742 ( 220) hydrogen bonds : angle 5.54996 ( 600) *********************** 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 386 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 332 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 450 GLN cc_start: 0.8561 (tm-30) cc_final: 0.7776 (tm-30) REVERT: F 451 MET cc_start: 0.7964 (tmm) cc_final: 0.7676 (tmm) REVERT: F 470 MET cc_start: 0.6898 (mtt) cc_final: 0.5949 (mtt) REVERT: F 500 GLU cc_start: 0.6354 (mp0) cc_final: 0.6057 (mp0) REVERT: F 512 ASN cc_start: 0.8129 (OUTLIER) cc_final: 0.7903 (t0) REVERT: F 515 MET cc_start: 0.6671 (OUTLIER) cc_final: 0.6222 (pp-130) REVERT: A 437 GLN cc_start: 0.7847 (mt0) cc_final: 0.6855 (mt0) REVERT: A 441 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7113 (tm-30) REVERT: A 450 GLN cc_start: 0.8798 (tm-30) cc_final: 0.7949 (tm-30) REVERT: A 457 ASN cc_start: 0.9090 (m-40) cc_final: 0.8828 (m-40) REVERT: A 458 GLN cc_start: 0.8398 (pt0) cc_final: 0.7779 (pt0) REVERT: A 473 ASP cc_start: 0.8382 (p0) cc_final: 0.7932 (p0) REVERT: A 482 THR cc_start: 0.8191 (t) cc_final: 0.7802 (t) REVERT: A 515 MET cc_start: 0.6522 (pp-130) cc_final: 0.5373 (pp-130) REVERT: B 443 LYS cc_start: 0.8837 (mmtp) cc_final: 0.8377 (mtpp) REVERT: B 450 GLN cc_start: 0.8663 (tm-30) cc_final: 0.7821 (tm-30) REVERT: B 451 MET cc_start: 0.8358 (tmm) cc_final: 0.7935 (tmm) REVERT: B 457 ASN cc_start: 0.9023 (m-40) cc_final: 0.8808 (m-40) REVERT: B 458 GLN cc_start: 0.8735 (pt0) cc_final: 0.8085 (pt0) REVERT: B 469 ILE cc_start: 0.8983 (tp) cc_final: 0.8632 (tt) REVERT: B 482 THR cc_start: 0.7764 (t) cc_final: 0.7382 (t) REVERT: B 515 MET cc_start: 0.7133 (OUTLIER) cc_final: 0.6879 (pp-130) REVERT: C 450 GLN cc_start: 0.8753 (tm-30) cc_final: 0.7809 (tm-30) REVERT: C 458 GLN cc_start: 0.8610 (pt0) cc_final: 0.8174 (pt0) REVERT: C 500 GLU cc_start: 0.6681 (mp0) cc_final: 0.6393 (mp0) REVERT: D 441 GLN cc_start: 0.7743 (mp10) cc_final: 0.7007 (mp10) REVERT: D 458 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7456 (pt0) REVERT: D 469 ILE cc_start: 0.8930 (tp) cc_final: 0.8637 (tt) REVERT: D 515 MET cc_start: 0.6780 (OUTLIER) cc_final: 0.6462 (pp-130) REVERT: E 439 TRP cc_start: 0.8033 (t60) cc_final: 0.7740 (t60) REVERT: E 443 LYS cc_start: 0.8789 (mmtt) cc_final: 0.8432 (mtpp) REVERT: E 450 GLN cc_start: 0.8623 (tm-30) cc_final: 0.7652 (tm-30) REVERT: E 451 MET cc_start: 0.8316 (tpp) cc_final: 0.7917 (tpt) REVERT: E 470 MET cc_start: 0.7250 (mtm) cc_final: 0.5909 (mtt) REVERT: E 472 GLU cc_start: 0.6202 (OUTLIER) cc_final: 0.5597 (pp20) REVERT: E 473 ASP cc_start: 0.8193 (p0) cc_final: 0.7927 (p0) REVERT: E 492 ASP cc_start: 0.8335 (p0) cc_final: 0.8012 (m-30) REVERT: E 500 GLU cc_start: 0.7071 (mp0) cc_final: 0.6841 (mp0) REVERT: E 507 GLN cc_start: 0.7248 (pm20) cc_final: 0.7034 (pm20) REVERT: G 439 TRP cc_start: 0.8285 (t60) cc_final: 0.7690 (t60) REVERT: G 450 GLN cc_start: 0.8871 (tm-30) cc_final: 0.8100 (tm-30) REVERT: G 458 GLN cc_start: 0.8623 (pt0) cc_final: 0.8079 (pt0) REVERT: G 515 MET cc_start: 0.6285 (pp-130) cc_final: 0.5540 (pp-130) REVERT: H 450 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8361 (tm-30) REVERT: H 451 MET cc_start: 0.8413 (tpt) cc_final: 0.7867 (tpt) REVERT: H 457 ASN cc_start: 0.8810 (m-40) cc_final: 0.8015 (t0) REVERT: H 458 GLN cc_start: 0.8879 (pt0) cc_final: 0.8396 (pt0) REVERT: H 470 MET cc_start: 0.7559 (mtp) cc_final: 0.6475 (mtp) REVERT: H 500 GLU cc_start: 0.6598 (mp0) cc_final: 0.6198 (mp0) REVERT: H 515 MET cc_start: 0.6686 (OUTLIER) cc_final: 0.6196 (pp-130) REVERT: I 450 GLN cc_start: 0.8723 (tm-30) cc_final: 0.7866 (tm-30) REVERT: I 451 MET cc_start: 0.8351 (tpt) cc_final: 0.7771 (tpt) REVERT: I 457 ASN cc_start: 0.8832 (m-40) cc_final: 0.8185 (t0) REVERT: I 458 GLN cc_start: 0.8833 (pt0) cc_final: 0.8346 (pt0) REVERT: I 473 ASP cc_start: 0.8112 (p0) cc_final: 0.7900 (p0) REVERT: I 482 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.8243 (t) REVERT: I 500 GLU cc_start: 0.6823 (mp0) cc_final: 0.6326 (mp0) REVERT: I 515 MET cc_start: 0.6630 (pp-130) cc_final: 0.5378 (pp-130) REVERT: J 441 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7720 (mp10) REVERT: J 457 ASN cc_start: 0.8661 (m-40) cc_final: 0.8228 (t0) REVERT: J 470 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.6717 (mtt) REVERT: J 472 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6534 (pp20) REVERT: J 473 ASP cc_start: 0.8573 (p0) cc_final: 0.8243 (p0) REVERT: J 500 GLU cc_start: 0.6438 (mp0) cc_final: 0.6109 (mp0) outliers start: 54 outliers final: 38 residues processed: 342 average time/residue: 0.0792 time to fit residues: 36.1159 Evaluate side-chains 372 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 322 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 453 GLU Chi-restraints excluded: chain F residue 460 LEU Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 512 ASN Chi-restraints excluded: chain F residue 515 MET Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 453 GLU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 477 VAL 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 482 THR 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 472 GLU Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 509 LEU Chi-restraints excluded: chain G residue 447 ILE 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 495 ASP Chi-restraints excluded: chain H residue 509 LEU Chi-restraints excluded: chain H residue 515 MET Chi-restraints excluded: chain I residue 453 GLU Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 504 VAL Chi-restraints excluded: chain I residue 509 LEU Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain J residue 447 ILE Chi-restraints excluded: chain J residue 453 GLU Chi-restraints excluded: chain J residue 460 LEU Chi-restraints excluded: chain J residue 470 MET Chi-restraints excluded: chain J residue 472 GLU Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 495 ASP 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 24 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 chunk 56 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 chunk 42 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 overall best weight: 4.5186 ------------------------------------------------------------------------------- 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 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 GLN ** D 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.128743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.114291 restraints weight = 13593.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.118005 restraints weight = 7397.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.120608 restraints weight = 4633.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.122351 restraints weight = 3144.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.123630 restraints weight = 2260.399| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6930 Z= 0.177 Angle : 0.948 11.554 9300 Z= 0.427 Chirality : 0.046 0.163 1100 Planarity : 0.003 0.025 1190 Dihedral : 5.507 15.573 900 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 7.09 % Allowed : 23.42 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.82 (0.26), residues: 840 helix: -2.52 (0.19), residues: 600 sheet: None (None), residues: 0 loop : -1.94 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 466 TYR 0.008 0.001 TYR F 474 PHE 0.015 0.004 PHE A 501 TRP 0.027 0.003 TRP F 439 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 6930) covalent geometry : angle 0.94754 ( 9300) hydrogen bonds : bond 0.03767 ( 220) hydrogen bonds : angle 5.57937 ( 600) *********************** 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 400 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 344 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 450 GLN cc_start: 0.8745 (tm-30) cc_final: 0.7900 (tm-30) REVERT: F 451 MET cc_start: 0.7997 (tmm) cc_final: 0.7705 (tmm) REVERT: F 470 MET cc_start: 0.6981 (mtt) cc_final: 0.6357 (mtt) REVERT: F 484 THR cc_start: 0.9104 (t) cc_final: 0.8746 (p) REVERT: F 500 GLU cc_start: 0.6374 (mp0) cc_final: 0.6042 (mp0) REVERT: F 512 ASN cc_start: 0.8225 (OUTLIER) cc_final: 0.8003 (t0) REVERT: F 515 MET cc_start: 0.6731 (OUTLIER) cc_final: 0.6207 (pp-130) REVERT: A 437 GLN cc_start: 0.7943 (mt0) cc_final: 0.6802 (mt0) REVERT: A 439 TRP cc_start: 0.8221 (t60) cc_final: 0.7961 (t60) REVERT: A 441 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7101 (tm-30) REVERT: A 450 GLN cc_start: 0.8798 (tm-30) cc_final: 0.7958 (tm-30) REVERT: A 457 ASN cc_start: 0.9103 (m-40) cc_final: 0.8869 (m-40) REVERT: A 458 GLN cc_start: 0.8376 (pt0) cc_final: 0.7690 (pt0) REVERT: A 473 ASP cc_start: 0.8440 (p0) cc_final: 0.7980 (p0) REVERT: A 482 THR cc_start: 0.8318 (t) cc_final: 0.7944 (t) REVERT: A 501 PHE cc_start: 0.8862 (t80) cc_final: 0.8568 (t80) REVERT: A 515 MET cc_start: 0.6596 (pp-130) cc_final: 0.5522 (pp-130) REVERT: B 443 LYS cc_start: 0.8871 (mmtp) cc_final: 0.8403 (mtpp) REVERT: B 450 GLN cc_start: 0.8690 (tm-30) cc_final: 0.7746 (tm-30) REVERT: B 451 MET cc_start: 0.8369 (tmm) cc_final: 0.7971 (tmm) REVERT: B 457 ASN cc_start: 0.9085 (m-40) cc_final: 0.8706 (m-40) REVERT: B 458 GLN cc_start: 0.8775 (pt0) cc_final: 0.8450 (pt0) REVERT: B 469 ILE cc_start: 0.9035 (tp) cc_final: 0.8756 (tt) REVERT: B 482 THR cc_start: 0.7760 (t) cc_final: 0.7362 (t) REVERT: B 500 GLU cc_start: 0.6831 (mp0) cc_final: 0.6595 (mp0) REVERT: B 515 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.6938 (pp-130) REVERT: C 450 GLN cc_start: 0.8718 (tm-30) cc_final: 0.7838 (tm-30) REVERT: C 482 THR cc_start: 0.8200 (OUTLIER) cc_final: 0.7878 (t) REVERT: C 488 ARG cc_start: 0.8572 (mtm180) cc_final: 0.8178 (mtm180) REVERT: C 500 GLU cc_start: 0.6801 (mp0) cc_final: 0.6503 (mp0) REVERT: D 441 GLN cc_start: 0.7795 (mp10) cc_final: 0.7422 (mp10) REVERT: D 444 ARG cc_start: 0.8732 (ttt180) cc_final: 0.8367 (ttt180) REVERT: D 450 GLN cc_start: 0.8626 (tm-30) cc_final: 0.7924 (tm-30) REVERT: D 451 MET cc_start: 0.7885 (tmm) cc_final: 0.7154 (tmm) REVERT: D 453 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8256 (tm-30) REVERT: D 458 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7479 (pt0) REVERT: D 469 ILE cc_start: 0.8972 (tp) cc_final: 0.8698 (tt) REVERT: D 489 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8722 (mm-40) REVERT: E 439 TRP cc_start: 0.8188 (t60) cc_final: 0.7779 (t60) REVERT: E 443 LYS cc_start: 0.8723 (mmtt) cc_final: 0.8391 (mtpp) REVERT: E 450 GLN cc_start: 0.8631 (tm-30) cc_final: 0.7544 (tm-30) REVERT: E 451 MET cc_start: 0.8258 (tpp) cc_final: 0.7830 (tpt) REVERT: E 470 MET cc_start: 0.7353 (mtm) cc_final: 0.5971 (mtt) REVERT: E 472 GLU cc_start: 0.6279 (OUTLIER) cc_final: 0.5575 (pp20) REVERT: E 473 ASP cc_start: 0.8257 (p0) cc_final: 0.7952 (p0) REVERT: E 492 ASP cc_start: 0.8329 (p0) cc_final: 0.7999 (m-30) REVERT: E 500 GLU cc_start: 0.7148 (mp0) cc_final: 0.6916 (mp0) REVERT: G 439 TRP cc_start: 0.8313 (t60) cc_final: 0.7779 (t60) REVERT: G 450 GLN cc_start: 0.8879 (tm-30) cc_final: 0.8125 (tm-30) REVERT: G 458 GLN cc_start: 0.8576 (pt0) cc_final: 0.8269 (pt0) REVERT: G 515 MET cc_start: 0.6679 (pp-130) cc_final: 0.6206 (pp-130) REVERT: H 450 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8322 (tm-30) REVERT: H 451 MET cc_start: 0.8365 (tpt) cc_final: 0.7791 (tpt) REVERT: H 457 ASN cc_start: 0.8917 (m-40) cc_final: 0.8034 (t0) REVERT: H 458 GLN cc_start: 0.8918 (pt0) cc_final: 0.8414 (pt0) REVERT: H 470 MET cc_start: 0.7647 (mtp) cc_final: 0.6552 (mtp) REVERT: H 500 GLU cc_start: 0.6749 (mp0) cc_final: 0.6340 (mp0) REVERT: H 515 MET cc_start: 0.7054 (OUTLIER) cc_final: 0.6491 (pp-130) REVERT: I 450 GLN cc_start: 0.8700 (tm-30) cc_final: 0.7865 (tm-30) REVERT: I 451 MET cc_start: 0.8337 (tpt) cc_final: 0.7756 (tpt) REVERT: I 457 ASN cc_start: 0.8868 (m-40) cc_final: 0.8235 (t0) REVERT: I 458 GLN cc_start: 0.8868 (pt0) cc_final: 0.8375 (pt0) REVERT: I 473 ASP cc_start: 0.8283 (p0) cc_final: 0.7949 (p0) REVERT: I 482 THR cc_start: 0.8414 (OUTLIER) cc_final: 0.8144 (t) REVERT: I 500 GLU cc_start: 0.6846 (mp0) cc_final: 0.6359 (mp0) REVERT: I 515 MET cc_start: 0.6798 (pp-130) cc_final: 0.5837 (pp-130) REVERT: J 441 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7739 (mp10) REVERT: J 450 GLN cc_start: 0.8866 (tm-30) cc_final: 0.8006 (tm-30) REVERT: J 457 ASN cc_start: 0.8695 (m-40) cc_final: 0.8285 (t0) REVERT: J 470 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.6606 (mtt) REVERT: J 472 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6629 (pp20) REVERT: J 473 ASP cc_start: 0.8607 (p0) cc_final: 0.8274 (p0) REVERT: J 500 GLU cc_start: 0.6523 (mp0) cc_final: 0.6199 (mp0) outliers start: 56 outliers final: 37 residues processed: 353 average time/residue: 0.0849 time to fit residues: 39.8024 Evaluate side-chains 383 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 332 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 453 GLU Chi-restraints excluded: chain F residue 456 LEU 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 512 ASN Chi-restraints excluded: chain F residue 515 MET Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 504 VAL 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 477 VAL 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 482 THR 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 489 GLN Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain E residue 472 GLU Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 509 LEU Chi-restraints excluded: chain G residue 447 ILE 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 495 ASP Chi-restraints excluded: chain H residue 509 LEU Chi-restraints excluded: chain H residue 515 MET Chi-restraints excluded: chain I residue 453 GLU Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain I residue 504 VAL Chi-restraints excluded: chain I residue 509 LEU Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain J residue 447 ILE Chi-restraints excluded: chain J residue 453 GLU Chi-restraints excluded: chain J residue 470 MET Chi-restraints excluded: chain J residue 472 GLU Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 495 ASP 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 32 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 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 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 438 GLN ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN ** C 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN D 489 GLN ** D 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 514 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 H 438 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.128156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.113901 restraints weight = 13567.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.117569 restraints weight = 7361.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.120010 restraints weight = 4588.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.121836 restraints weight = 3163.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.123143 restraints weight = 2255.785| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.5644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6930 Z= 0.188 Angle : 0.996 12.960 9300 Z= 0.452 Chirality : 0.048 0.167 1100 Planarity : 0.003 0.032 1190 Dihedral : 5.597 15.742 900 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 21.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 7.22 % Allowed : 24.81 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.15 (0.28), residues: 840 helix: -2.45 (0.19), residues: 550 sheet: None (None), residues: 0 loop : -0.86 (0.40), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 466 TYR 0.010 0.002 TYR F 474 PHE 0.013 0.003 PHE A 501 TRP 0.033 0.003 TRP F 439 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 6930) covalent geometry : angle 0.99605 ( 9300) hydrogen bonds : bond 0.04041 ( 220) hydrogen bonds : angle 5.64816 ( 600) ********************** 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 398 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 341 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 450 GLN cc_start: 0.8704 (tm-30) cc_final: 0.7903 (tm-30) REVERT: F 451 MET cc_start: 0.7922 (tmm) cc_final: 0.7630 (tmm) REVERT: F 453 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8396 (tm-30) REVERT: F 484 THR cc_start: 0.9115 (t) cc_final: 0.8765 (p) REVERT: F 500 GLU cc_start: 0.6410 (mp0) cc_final: 0.6073 (mp0) REVERT: F 515 MET cc_start: 0.6427 (OUTLIER) cc_final: 0.5939 (pp-130) REVERT: A 437 GLN cc_start: 0.8084 (mt0) cc_final: 0.6897 (mt0) REVERT: A 439 TRP cc_start: 0.8274 (t60) cc_final: 0.7977 (t60) REVERT: A 441 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.6964 (tm-30) REVERT: A 450 GLN cc_start: 0.8868 (tm-30) cc_final: 0.7987 (tm-30) REVERT: A 453 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7955 (tm-30) REVERT: A 457 ASN cc_start: 0.9113 (m-40) cc_final: 0.8484 (m-40) REVERT: A 458 GLN cc_start: 0.8402 (pt0) cc_final: 0.7728 (pt0) REVERT: A 473 ASP cc_start: 0.8470 (p0) cc_final: 0.8091 (p0) REVERT: A 482 THR cc_start: 0.8314 (t) cc_final: 0.7946 (t) REVERT: A 501 PHE cc_start: 0.8901 (t80) cc_final: 0.8646 (t80) REVERT: A 515 MET cc_start: 0.6745 (pp-130) cc_final: 0.5677 (pp-130) REVERT: B 443 LYS cc_start: 0.8930 (mmtp) cc_final: 0.8442 (mtpp) REVERT: B 450 GLN cc_start: 0.8685 (tm-30) cc_final: 0.7782 (tm-30) REVERT: B 451 MET cc_start: 0.8353 (tmm) cc_final: 0.7947 (tmm) REVERT: B 457 ASN cc_start: 0.9118 (m-40) cc_final: 0.8700 (m-40) REVERT: B 458 GLN cc_start: 0.8827 (pt0) cc_final: 0.8568 (pt0) REVERT: B 482 THR cc_start: 0.7821 (t) cc_final: 0.7439 (t) REVERT: B 500 GLU cc_start: 0.6791 (mp0) cc_final: 0.6576 (mp0) REVERT: C 450 GLN cc_start: 0.8721 (tm-30) cc_final: 0.7847 (tm-30) REVERT: C 458 GLN cc_start: 0.8622 (pt0) cc_final: 0.8235 (pt0) REVERT: C 488 ARG cc_start: 0.8597 (mtm180) cc_final: 0.8197 (mtm180) REVERT: D 441 GLN cc_start: 0.7769 (mp10) cc_final: 0.7565 (mp10) REVERT: D 444 ARG cc_start: 0.8696 (ttt180) cc_final: 0.8204 (ttt180) REVERT: D 450 GLN cc_start: 0.8574 (tm-30) cc_final: 0.7887 (tm-30) REVERT: D 451 MET cc_start: 0.7886 (tmm) cc_final: 0.7150 (tmm) REVERT: D 453 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8277 (tm-30) REVERT: D 458 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7494 (pt0) REVERT: D 469 ILE cc_start: 0.9050 (tp) cc_final: 0.8810 (tt) REVERT: D 489 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8763 (mm-40) REVERT: E 439 TRP cc_start: 0.8100 (t60) cc_final: 0.7714 (t60) REVERT: E 443 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8375 (mtpp) REVERT: E 450 GLN cc_start: 0.8612 (tm-30) cc_final: 0.8193 (tm-30) REVERT: E 451 MET cc_start: 0.8309 (tpp) cc_final: 0.7942 (tpt) REVERT: E 470 MET cc_start: 0.7372 (mtm) cc_final: 0.6292 (mtt) REVERT: E 492 ASP cc_start: 0.8294 (p0) cc_final: 0.7989 (m-30) REVERT: E 500 GLU cc_start: 0.7165 (mp0) cc_final: 0.6925 (mp0) REVERT: G 439 TRP cc_start: 0.8313 (t60) cc_final: 0.7780 (t60) REVERT: G 450 GLN cc_start: 0.8886 (tm-30) cc_final: 0.8128 (tm-30) REVERT: G 458 GLN cc_start: 0.8484 (pt0) cc_final: 0.7926 (pt0) REVERT: G 515 MET cc_start: 0.6829 (pp-130) cc_final: 0.6361 (pp-130) REVERT: H 450 GLN cc_start: 0.8806 (tm-30) cc_final: 0.8312 (tm-30) REVERT: H 451 MET cc_start: 0.8422 (tpt) cc_final: 0.7800 (tpt) REVERT: H 457 ASN cc_start: 0.8907 (m-40) cc_final: 0.8074 (t0) REVERT: H 458 GLN cc_start: 0.8920 (pt0) cc_final: 0.8417 (pt0) REVERT: H 470 MET cc_start: 0.7513 (mtp) cc_final: 0.6279 (mtp) REVERT: H 500 GLU cc_start: 0.6792 (mp0) cc_final: 0.6313 (mp0) REVERT: I 450 GLN cc_start: 0.8761 (tm-30) cc_final: 0.7950 (tm-30) REVERT: I 451 MET cc_start: 0.8340 (tpt) cc_final: 0.7746 (tpt) REVERT: I 457 ASN cc_start: 0.8870 (m-40) cc_final: 0.8235 (t0) REVERT: I 458 GLN cc_start: 0.8865 (pt0) cc_final: 0.8358 (pt0) REVERT: I 473 ASP cc_start: 0.8308 (p0) cc_final: 0.8017 (p0) REVERT: I 482 THR cc_start: 0.8404 (OUTLIER) cc_final: 0.8094 (t) REVERT: I 500 GLU cc_start: 0.6864 (mp0) cc_final: 0.6372 (mp0) REVERT: I 515 MET cc_start: 0.6581 (pp-130) cc_final: 0.5758 (pp-130) REVERT: J 441 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7720 (mp10) REVERT: J 450 GLN cc_start: 0.8831 (tm-30) cc_final: 0.7893 (tm-30) REVERT: J 457 ASN cc_start: 0.8766 (m-40) cc_final: 0.8133 (t0) REVERT: J 470 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6476 (mtt) REVERT: J 472 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6703 (pp20) REVERT: J 473 ASP cc_start: 0.8648 (p0) cc_final: 0.8298 (p0) REVERT: J 500 GLU cc_start: 0.6535 (mp0) cc_final: 0.6203 (mp0) outliers start: 57 outliers final: 37 residues processed: 354 average time/residue: 0.0826 time to fit residues: 38.8425 Evaluate side-chains 378 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 330 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 453 GLU Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 460 LEU 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 441 GLN Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 504 VAL 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 477 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 458 GLN Chi-restraints excluded: chain D residue 489 GLN Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 504 VAL Chi-restraints excluded: chain E residue 509 LEU Chi-restraints excluded: chain G residue 447 ILE 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 509 LEU Chi-restraints excluded: chain I residue 453 GLU Chi-restraints excluded: chain I residue 482 THR Chi-restraints excluded: chain I residue 491 LEU Chi-restraints excluded: chain I residue 504 VAL Chi-restraints excluded: chain I residue 509 LEU Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain J residue 447 ILE Chi-restraints excluded: chain J residue 453 GLU Chi-restraints excluded: chain J residue 470 MET Chi-restraints excluded: chain J residue 472 GLU Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 495 ASP 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 30 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 63 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN D 489 GLN D 512 ASN ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.133050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.118398 restraints weight = 13458.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.122231 restraints weight = 7244.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.124861 restraints weight = 4491.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.126669 restraints weight = 3043.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.127953 restraints weight = 2184.379| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.5862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6930 Z= 0.148 Angle : 0.976 13.033 9300 Z= 0.437 Chirality : 0.046 0.194 1100 Planarity : 0.003 0.031 1190 Dihedral : 5.411 15.670 900 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 5.32 % Allowed : 26.84 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.69 (0.26), residues: 840 helix: -2.40 (0.19), residues: 600 sheet: None (None), residues: 0 loop : -1.96 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 466 TYR 0.010 0.001 TYR F 474 PHE 0.009 0.003 PHE A 501 TRP 0.030 0.003 TRP J 439 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 6930) covalent geometry : angle 0.97628 ( 9300) hydrogen bonds : bond 0.03929 ( 220) hydrogen bonds : angle 5.51296 ( 600) =============================================================================== Job complete usr+sys time: 1264.86 seconds wall clock time: 22 minutes 45.87 seconds (1365.87 seconds total)