Starting phenix.real_space_refine on Fri Sep 11 05:36:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5yrn_6842/09_2026/5yrn_6842.cif Found real_map, /net/cci-nas-00/data/ceres_data/5yrn_6842/09_2026/5yrn_6842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5yrn_6842/09_2026/5yrn_6842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5yrn_6842/09_2026/5yrn_6842.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5yrn_6842/09_2026/5yrn_6842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5yrn_6842/09_2026/5yrn_6842.map" } resolution = 4.1 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= 0.001 sd= 0.005 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 48 5.16 5 C 5100 2.51 5 N 1452 2.21 5 O 1680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8280 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 1.09, per 1000 atoms: 0.13 Number of scatterers: 8280 At special positions: 0 Unit cell: (89.79, 89.79, 95.94, 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 48 16.00 O 1680 8.00 N 1452 7.00 C 5100 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: 0.65 Conformation dependent library (CDL) restraints added in 377.3 milliseconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 87.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 430 through 443 removed outlier: 3.773A pdb=" N GLN A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 451 Processing helix chain 'A' and resid 452 through 466 removed outlier: 3.573A pdb=" N SER A 459 " --> pdb=" O CYS A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 479 Processing helix chain 'A' and resid 482 through 497 removed outlier: 3.523A pdb=" N GLN A 489 " --> pdb=" O SER A 485 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 490 " --> pdb=" O LYS A 486 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A 496 " --> pdb=" O ASP A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 512 removed outlier: 3.773A pdb=" N VAL A 504 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE A 505 " --> pdb=" O PHE A 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 removed outlier: 3.772A pdb=" N GLN B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 451 Processing helix chain 'B' and resid 452 through 466 removed outlier: 3.574A pdb=" N SER B 459 " --> pdb=" O CYS B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 479 Processing helix chain 'B' and resid 482 through 497 removed outlier: 3.522A pdb=" N GLN B 489 " --> pdb=" O SER B 485 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 490 " --> pdb=" O LYS B 486 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 496 " --> pdb=" O ASP B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 512 removed outlier: 3.774A pdb=" N VAL B 504 " --> pdb=" O GLU B 500 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE B 505 " --> pdb=" O PHE B 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 443 removed outlier: 3.773A pdb=" N GLN C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 451 Processing helix chain 'C' and resid 452 through 466 removed outlier: 3.573A pdb=" N SER C 459 " --> pdb=" O CYS C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 479 Processing helix chain 'C' and resid 482 through 497 removed outlier: 3.523A pdb=" N GLN C 489 " --> pdb=" O SER C 485 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 490 " --> pdb=" O LYS C 486 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE C 496 " --> pdb=" O ASP C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 512 removed outlier: 3.773A pdb=" N VAL C 504 " --> pdb=" O GLU C 500 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE C 505 " --> pdb=" O PHE C 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 443 removed outlier: 3.772A pdb=" N GLN D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 451 Processing helix chain 'D' and resid 452 through 466 removed outlier: 3.573A pdb=" N SER D 459 " --> pdb=" O CYS D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 479 Processing helix chain 'D' and resid 482 through 497 removed outlier: 3.522A pdb=" N GLN D 489 " --> pdb=" O SER D 485 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU D 490 " --> pdb=" O LYS D 486 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE D 496 " --> pdb=" O ASP D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 512 removed outlier: 3.773A pdb=" N VAL D 504 " --> pdb=" O GLU D 500 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE D 505 " --> pdb=" O PHE D 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 443 removed outlier: 3.773A pdb=" N GLN E 437 " --> pdb=" O ALA E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 451 Processing helix chain 'E' and resid 452 through 466 removed outlier: 3.573A pdb=" N SER E 459 " --> pdb=" O CYS E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 479 Processing helix chain 'E' and resid 482 through 497 removed outlier: 3.523A pdb=" N GLN E 489 " --> pdb=" O SER E 485 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU E 490 " --> pdb=" O LYS E 486 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP E 495 " --> pdb=" O LEU E 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE E 496 " --> pdb=" O ASP E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 512 removed outlier: 3.773A pdb=" N VAL E 504 " --> pdb=" O GLU E 500 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE E 505 " --> pdb=" O PHE E 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 443 removed outlier: 3.773A pdb=" N GLN F 437 " --> pdb=" O ALA F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 444 through 451 Processing helix chain 'F' and resid 452 through 466 removed outlier: 3.573A pdb=" N SER F 459 " --> pdb=" O CYS F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 479 Processing helix chain 'F' and resid 482 through 497 removed outlier: 3.523A pdb=" N GLN F 489 " --> pdb=" O SER F 485 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU F 490 " --> pdb=" O LYS F 486 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP F 495 " --> pdb=" O LEU F 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE F 496 " --> pdb=" O ASP F 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 512 removed outlier: 3.774A pdb=" N VAL F 504 " --> pdb=" O GLU F 500 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE F 505 " --> pdb=" O PHE F 501 " (cutoff:3.500A) Processing helix chain 'G' and resid 431 through 443 removed outlier: 3.772A pdb=" N GLN G 437 " --> pdb=" O ALA G 433 " (cutoff:3.500A) Processing helix chain 'G' and resid 444 through 451 Processing helix chain 'G' and resid 452 through 466 removed outlier: 3.574A pdb=" N SER G 459 " --> pdb=" O CYS G 455 " (cutoff:3.500A) Processing helix chain 'G' and resid 470 through 479 Processing helix chain 'G' and resid 482 through 497 removed outlier: 3.523A pdb=" N GLN G 489 " --> pdb=" O SER G 485 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU G 490 " --> pdb=" O LYS G 486 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP G 495 " --> pdb=" O LEU G 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE G 496 " --> pdb=" O ASP G 492 " (cutoff:3.500A) Processing helix chain 'G' and resid 499 through 512 removed outlier: 3.774A pdb=" N VAL G 504 " --> pdb=" O GLU G 500 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE G 505 " --> pdb=" O PHE G 501 " (cutoff:3.500A) Processing helix chain 'H' and resid 431 through 443 removed outlier: 3.773A pdb=" N GLN H 437 " --> pdb=" O ALA H 433 " (cutoff:3.500A) Processing helix chain 'H' and resid 444 through 451 Processing helix chain 'H' and resid 452 through 466 removed outlier: 3.573A pdb=" N SER H 459 " --> pdb=" O CYS H 455 " (cutoff:3.500A) Processing helix chain 'H' and resid 470 through 479 Processing helix chain 'H' and resid 482 through 497 removed outlier: 3.522A pdb=" N GLN H 489 " --> pdb=" O SER H 485 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU H 490 " --> pdb=" O LYS H 486 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP H 495 " --> pdb=" O LEU H 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE H 496 " --> pdb=" O ASP H 492 " (cutoff:3.500A) Processing helix chain 'H' and resid 499 through 512 removed outlier: 3.773A pdb=" N VAL H 504 " --> pdb=" O GLU H 500 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE H 505 " --> pdb=" O PHE H 501 " (cutoff:3.500A) Processing helix chain 'I' and resid 431 through 443 removed outlier: 3.773A pdb=" N GLN I 437 " --> pdb=" O ALA I 433 " (cutoff:3.500A) Processing helix chain 'I' and resid 444 through 451 Processing helix chain 'I' and resid 452 through 466 removed outlier: 3.573A pdb=" N SER I 459 " --> pdb=" O CYS I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 470 through 479 Processing helix chain 'I' and resid 482 through 497 removed outlier: 3.523A pdb=" N GLN I 489 " --> pdb=" O SER I 485 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU I 490 " --> pdb=" O LYS I 486 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP I 495 " --> pdb=" O LEU I 491 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE I 496 " --> pdb=" O ASP I 492 " (cutoff:3.500A) Processing helix chain 'I' and resid 499 through 512 removed outlier: 3.774A pdb=" N VAL I 504 " --> pdb=" O GLU I 500 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE I 505 " --> pdb=" O PHE I 501 " (cutoff:3.500A) Processing helix chain 'J' and resid 431 through 443 removed outlier: 3.772A pdb=" N GLN J 437 " --> pdb=" O ALA J 433 " (cutoff:3.500A) Processing helix chain 'J' and resid 444 through 451 Processing helix chain 'J' and resid 452 through 466 removed outlier: 3.574A pdb=" N SER J 459 " --> pdb=" O CYS J 455 " (cutoff:3.500A) Processing helix chain 'J' and resid 470 through 479 Processing helix chain 'J' and resid 482 through 497 removed outlier: 3.523A pdb=" N GLN J 489 " --> pdb=" O SER J 485 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU J 490 " --> pdb=" O LYS J 486 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP J 495 " --> pdb=" O LEU J 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE J 496 " --> pdb=" O ASP J 492 " (cutoff:3.500A) Processing helix chain 'J' and resid 499 through 512 removed outlier: 3.773A pdb=" N VAL J 504 " --> pdb=" O GLU J 500 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE J 505 " --> pdb=" O PHE J 501 " (cutoff:3.500A) Processing helix chain 'K' and resid 431 through 443 removed outlier: 3.772A pdb=" N GLN K 437 " --> pdb=" O ALA K 433 " (cutoff:3.500A) Processing helix chain 'K' and resid 444 through 451 Processing helix chain 'K' and resid 452 through 466 removed outlier: 3.573A pdb=" N SER K 459 " --> pdb=" O CYS K 455 " (cutoff:3.500A) Processing helix chain 'K' and resid 470 through 479 Processing helix chain 'K' and resid 482 through 497 removed outlier: 3.522A pdb=" N GLN K 489 " --> pdb=" O SER K 485 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU K 490 " --> pdb=" O LYS K 486 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP K 495 " --> pdb=" O LEU K 491 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE K 496 " --> pdb=" O ASP K 492 " (cutoff:3.500A) Processing helix chain 'K' and resid 499 through 512 removed outlier: 3.773A pdb=" N VAL K 504 " --> pdb=" O GLU K 500 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE K 505 " --> pdb=" O PHE K 501 " (cutoff:3.500A) Processing helix chain 'L' and resid 431 through 443 removed outlier: 3.773A pdb=" N GLN L 437 " --> pdb=" O ALA L 433 " (cutoff:3.500A) Processing helix chain 'L' and resid 444 through 451 Processing helix chain 'L' and resid 452 through 466 removed outlier: 3.573A pdb=" N SER L 459 " --> pdb=" O CYS L 455 " (cutoff:3.500A) Processing helix chain 'L' and resid 470 through 479 Processing helix chain 'L' and resid 482 through 497 removed outlier: 3.522A pdb=" N GLN L 489 " --> pdb=" O SER L 485 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU L 490 " --> pdb=" O LYS L 486 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP L 495 " --> pdb=" O LEU L 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE L 496 " --> pdb=" O ASP L 492 " (cutoff:3.500A) Processing helix chain 'L' and resid 499 through 512 removed outlier: 3.773A pdb=" N VAL L 504 " --> pdb=" O GLU L 500 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE L 505 " --> pdb=" O PHE L 501 " (cutoff:3.500A) 529 hydrogen bonds defined for protein. 1587 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.19 Time building geometry restraints manager: 0.89 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: 2681 1.34 - 1.45: 809 1.45 - 1.57: 4754 1.57 - 1.69: 0 1.69 - 1.80: 84 Bond restraints: 8328 Sorted by residual: bond pdb=" N LYS G 443 " pdb=" CA LYS G 443 " ideal model delta sigma weight residual 1.463 1.437 0.026 1.36e-02 5.41e+03 3.56e+00 bond pdb=" N LYS L 443 " pdb=" CA LYS L 443 " ideal model delta sigma weight residual 1.463 1.438 0.025 1.36e-02 5.41e+03 3.49e+00 bond pdb=" N LYS D 443 " pdb=" CA LYS D 443 " ideal model delta sigma weight residual 1.463 1.438 0.025 1.36e-02 5.41e+03 3.41e+00 bond pdb=" N LYS C 443 " pdb=" CA LYS C 443 " ideal model delta sigma weight residual 1.463 1.438 0.025 1.36e-02 5.41e+03 3.40e+00 bond pdb=" N LYS H 443 " pdb=" CA LYS H 443 " ideal model delta sigma weight residual 1.463 1.438 0.025 1.36e-02 5.41e+03 3.37e+00 ... (remaining 8323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 8816 1.04 - 2.08: 1846 2.08 - 3.12: 318 3.12 - 4.15: 156 4.15 - 5.19: 48 Bond angle restraints: 11184 Sorted by residual: angle pdb=" C GLN J 514 " pdb=" N MET J 515 " pdb=" CA MET J 515 " ideal model delta sigma weight residual 122.40 126.32 -3.92 1.45e+00 4.76e-01 7.29e+00 angle pdb=" C GLN H 514 " pdb=" N MET H 515 " pdb=" CA MET H 515 " ideal model delta sigma weight residual 122.40 126.30 -3.90 1.45e+00 4.76e-01 7.25e+00 angle pdb=" C GLN E 514 " pdb=" N MET E 515 " pdb=" CA MET E 515 " ideal model delta sigma weight residual 122.40 126.30 -3.90 1.45e+00 4.76e-01 7.24e+00 angle pdb=" C GLN C 514 " pdb=" N MET C 515 " pdb=" CA MET C 515 " ideal model delta sigma weight residual 122.40 126.30 -3.90 1.45e+00 4.76e-01 7.24e+00 angle pdb=" C GLN B 514 " pdb=" N MET B 515 " pdb=" CA MET B 515 " ideal model delta sigma weight residual 122.40 126.30 -3.90 1.45e+00 4.76e-01 7.22e+00 ... (remaining 11179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.42: 4919 13.42 - 26.83: 265 26.83 - 40.25: 60 40.25 - 53.66: 36 53.66 - 67.08: 12 Dihedral angle restraints: 5292 sinusoidal: 2232 harmonic: 3060 Sorted by residual: dihedral pdb=" CA LEU D 456 " pdb=" C LEU D 456 " pdb=" N ASN D 457 " pdb=" CA ASN D 457 " ideal model delta harmonic sigma weight residual -180.00 -159.85 -20.15 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA LEU H 456 " pdb=" C LEU H 456 " pdb=" N ASN H 457 " pdb=" CA ASN H 457 " ideal model delta harmonic sigma weight residual 180.00 -159.88 -20.12 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA LEU A 456 " pdb=" C LEU A 456 " pdb=" N ASN A 457 " pdb=" CA ASN A 457 " ideal model delta harmonic sigma weight residual 180.00 -159.88 -20.12 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 5289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 848 0.040 - 0.080: 340 0.080 - 0.120: 108 0.120 - 0.160: 24 0.160 - 0.199: 12 Chirality restraints: 1332 Sorted by residual: chirality pdb=" CB ILE L 469 " pdb=" CA ILE L 469 " pdb=" CG1 ILE L 469 " pdb=" CG2 ILE L 469 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.95e-01 chirality pdb=" CB ILE B 469 " pdb=" CA ILE B 469 " pdb=" CG1 ILE B 469 " pdb=" CG2 ILE B 469 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.86e-01 chirality pdb=" CB ILE H 469 " pdb=" CA ILE H 469 " pdb=" CG1 ILE H 469 " pdb=" CG2 ILE H 469 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.84e-01 ... (remaining 1329 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL L 477 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C VAL L 477 " 0.024 2.00e-02 2.50e+03 pdb=" O VAL L 477 " -0.009 2.00e-02 2.50e+03 pdb=" N SER L 478 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 477 " 0.007 2.00e-02 2.50e+03 1.35e-02 1.81e+00 pdb=" C VAL F 477 " -0.023 2.00e-02 2.50e+03 pdb=" O VAL F 477 " 0.009 2.00e-02 2.50e+03 pdb=" N SER F 478 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL J 477 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.81e+00 pdb=" C VAL J 477 " 0.023 2.00e-02 2.50e+03 pdb=" O VAL J 477 " -0.009 2.00e-02 2.50e+03 pdb=" N SER J 478 " -0.008 2.00e-02 2.50e+03 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 3005 2.89 - 3.40: 9513 3.40 - 3.90: 13326 3.90 - 4.40: 16411 4.40 - 4.90: 24944 Nonbonded interactions: 67199 Sorted by model distance: nonbonded pdb=" NE2 GLN J 441 " pdb=" OD1 ASP J 495 " model vdw 2.393 3.120 nonbonded pdb=" NE2 GLN C 441 " pdb=" OD1 ASP C 495 " model vdw 2.393 3.120 nonbonded pdb=" NE2 GLN E 441 " pdb=" OD1 ASP E 495 " model vdw 2.393 3.120 nonbonded pdb=" NE2 GLN F 441 " pdb=" OD1 ASP F 495 " model vdw 2.393 3.120 nonbonded pdb=" NE2 GLN I 441 " pdb=" OD1 ASP I 495 " model vdw 2.393 3.120 ... (remaining 67194 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.680 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.920 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5556 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 : 0.007 0.034 8328 Z= 0.325 Angle : 1.001 5.193 11184 Z= 0.590 Chirality : 0.051 0.199 1332 Planarity : 0.005 0.022 1440 Dihedral : 10.654 67.080 3276 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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 are not related in a simple way. whole: -3.39 (0.21), residues: 1020 helix: -2.55 (0.13), residues: 780 sheet: None (None), residues: 0 loop : -0.14 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG L 444 TYR 0.003 0.001 TYR B 474 PHE 0.007 0.003 PHE K 501 TRP 0.020 0.004 TRP I 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00702 / 0.33 ( 8328) covalent geometry : angle 1.00099 / 0.59 (11184) hydrogen bonds : bond 0.30098 / 19.46 ( 529) hydrogen bonds : angle 8.51466 / 6.28 ( 1587) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 417 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 VAL cc_start: 0.7278 (t) cc_final: 0.6781 (t) REVERT: B 503 LYS cc_start: 0.8979 (ttmt) cc_final: 0.8663 (tptt) REVERT: C 470 MET cc_start: 0.4199 (mtm) cc_final: 0.3705 (mtt) REVERT: C 488 ARG cc_start: 0.6586 (mtt-85) cc_final: 0.6150 (tpp-160) REVERT: E 500 GLU cc_start: 0.8194 (tt0) cc_final: 0.7511 (pm20) REVERT: F 448 VAL cc_start: 0.6924 (t) cc_final: 0.6678 (t) REVERT: F 488 ARG cc_start: 0.4001 (mtt-85) cc_final: 0.3109 (mmp80) REVERT: H 456 LEU cc_start: 0.7744 (tp) cc_final: 0.7532 (tp) REVERT: H 471 LYS cc_start: 0.7596 (tttt) cc_final: 0.7164 (pttt) REVERT: J 435 ILE cc_start: 0.7045 (mt) cc_final: 0.6634 (tp) REVERT: J 438 GLN cc_start: 0.8938 (tt0) cc_final: 0.8726 (pt0) REVERT: L 441 GLN cc_start: 0.8602 (mt0) cc_final: 0.7993 (tm-30) REVERT: L 453 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7371 (tm-30) REVERT: L 460 LEU cc_start: 0.8505 (mt) cc_final: 0.8242 (mt) REVERT: L 470 MET cc_start: 0.7397 (mtm) cc_final: 0.7028 (mpp) REVERT: L 480 LYS cc_start: 0.7864 (mmtt) cc_final: 0.7544 (mmtt) REVERT: L 501 PHE cc_start: 0.8730 (t80) cc_final: 0.8433 (t80) outliers start: 0 outliers final: 0 residues processed: 417 average time/residue: 0.1371 time to fit residues: 71.1136 Evaluate side-chains 219 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.0070 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 GLN B 489 GLN B 497 GLN C 437 GLN C 458 GLN C 497 GLN ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 497 GLN I 458 GLN L 512 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.087267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.070691 restraints weight = 33049.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.072925 restraints weight = 23482.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.074672 restraints weight = 18046.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.075844 restraints weight = 14575.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.076972 restraints weight = 12373.334| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6162 moved from start: 0.6825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8328 Z= 0.164 Angle : 0.716 9.806 11184 Z= 0.382 Chirality : 0.043 0.203 1332 Planarity : 0.005 0.086 1440 Dihedral : 5.577 21.393 1092 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % 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 are not related in a simple way. whole: -1.69 (0.21), residues: 1020 helix: -0.99 (0.14), residues: 840 sheet: None (None), residues: 0 loop : -0.72 (0.39), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 483 TYR 0.008 0.001 TYR L 474 PHE 0.008 0.002 PHE J 501 TRP 0.015 0.002 TRP B 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 8328) covalent geometry : angle 0.71590 / 0.38 (11184) hydrogen bonds : bond 0.04689 / 3.08 ( 529) hydrogen bonds : angle 4.46178 / 3.30 ( 1587) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 LYS cc_start: 0.7816 (ptmm) cc_final: 0.7215 (pmmt) REVERT: A 476 LEU cc_start: 0.9197 (mt) cc_final: 0.8842 (mt) REVERT: A 484 THR cc_start: 0.9172 (p) cc_final: 0.8960 (p) REVERT: A 492 ASP cc_start: 0.8178 (m-30) cc_final: 0.7887 (m-30) REVERT: A 494 THR cc_start: 0.9024 (m) cc_final: 0.8715 (m) REVERT: B 460 LEU cc_start: 0.7493 (mt) cc_final: 0.7266 (mt) REVERT: B 483 ARG cc_start: 0.6669 (mtt90) cc_final: 0.6204 (ttt-90) REVERT: B 503 LYS cc_start: 0.9109 (ttmt) cc_final: 0.8755 (tptt) REVERT: C 480 LYS cc_start: 0.8589 (mptt) cc_final: 0.8322 (mmtm) REVERT: C 488 ARG cc_start: 0.8108 (mtt-85) cc_final: 0.7170 (mmt180) REVERT: C 503 LYS cc_start: 0.8152 (ttmt) cc_final: 0.7683 (tptt) REVERT: C 513 LYS cc_start: 0.8303 (mmmt) cc_final: 0.8012 (tppt) REVERT: D 446 ASP cc_start: 0.8655 (m-30) cc_final: 0.8380 (m-30) REVERT: D 488 ARG cc_start: 0.8384 (mmm-85) cc_final: 0.8176 (mtt-85) REVERT: D 503 LYS cc_start: 0.8678 (pttm) cc_final: 0.7567 (tptt) REVERT: D 513 LYS cc_start: 0.8511 (pptt) cc_final: 0.7935 (tptp) REVERT: E 461 ASP cc_start: 0.8767 (m-30) cc_final: 0.8394 (t70) REVERT: E 480 LYS cc_start: 0.8441 (mtpt) cc_final: 0.8024 (mtmt) REVERT: E 483 ARG cc_start: 0.7377 (mtt180) cc_final: 0.6909 (ttm-80) REVERT: E 503 LYS cc_start: 0.9101 (ptpp) cc_final: 0.8777 (pttp) REVERT: F 451 MET cc_start: 0.7252 (ttp) cc_final: 0.7052 (tpp) REVERT: G 475 GLU cc_start: 0.7486 (mp0) cc_final: 0.7075 (mt-10) REVERT: H 477 VAL cc_start: 0.6214 (t) cc_final: 0.4572 (p) REVERT: J 435 ILE cc_start: 0.7364 (mt) cc_final: 0.6852 (tp) REVERT: J 445 GLU cc_start: 0.7319 (mp0) cc_final: 0.6412 (mp0) REVERT: J 446 ASP cc_start: 0.8426 (t0) cc_final: 0.8218 (t0) REVERT: J 460 LEU cc_start: 0.7949 (mt) cc_final: 0.7688 (mt) REVERT: J 477 VAL cc_start: 0.4309 (t) cc_final: 0.3432 (t) REVERT: J 499 GLU cc_start: 0.8111 (pp20) cc_final: 0.7320 (tp30) REVERT: L 430 THR cc_start: 0.8075 (p) cc_final: 0.7715 (t) REVERT: L 453 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8024 (tm-30) REVERT: L 473 ASP cc_start: 0.6694 (m-30) cc_final: 0.5698 (m-30) REVERT: L 501 PHE cc_start: 0.8767 (t80) cc_final: 0.8480 (t80) outliers start: 0 outliers final: 0 residues processed: 324 average time/residue: 0.1195 time to fit residues: 50.0762 Evaluate side-chains 223 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 94 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 56 optimal weight: 30.0000 chunk 49 optimal weight: 0.9990 chunk 40 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 GLN A 512 ASN B 458 GLN C 497 GLN D 458 GLN E 497 GLN F 437 GLN F 449 ASN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 ASN G 514 GLN H 437 GLN H 441 GLN ** H 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 512 ASN H 514 GLN ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 441 GLN K 512 ASN K 514 GLN L 497 GLN L 512 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.082960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.067433 restraints weight = 34823.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.069635 restraints weight = 24536.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.071359 restraints weight = 18643.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.072700 restraints weight = 14826.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.073708 restraints weight = 12234.665| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 1.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8328 Z= 0.202 Angle : 0.773 6.371 11184 Z= 0.418 Chirality : 0.044 0.233 1332 Planarity : 0.005 0.059 1440 Dihedral : 5.646 27.829 1092 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.32 % Allowed : 5.59 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.23), residues: 1020 helix: -0.82 (0.15), residues: 924 sheet: None (None), residues: 0 loop : -2.30 (0.43), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 488 TYR 0.014 0.002 TYR L 474 PHE 0.012 0.003 PHE A 501 TRP 0.019 0.002 TRP J 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 ( 8328) covalent geometry : angle 0.77264 / 0.42 (11184) hydrogen bonds : bond 0.04696 / 3.08 ( 529) hydrogen bonds : angle 4.62810 / 3.42 ( 1587) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 398 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 LYS cc_start: 0.7899 (ptmm) cc_final: 0.7476 (ptmt) REVERT: A 461 ASP cc_start: 0.9013 (m-30) cc_final: 0.8644 (m-30) REVERT: A 471 LYS cc_start: 0.9232 (ptpp) cc_final: 0.8732 (ptmm) REVERT: A 480 LYS cc_start: 0.9500 (mmtt) cc_final: 0.9118 (mmmt) REVERT: A 486 LYS cc_start: 0.9388 (mtpt) cc_final: 0.9138 (mtmm) REVERT: A 488 ARG cc_start: 0.7919 (mtt-85) cc_final: 0.7682 (mtt90) REVERT: A 489 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8263 (tm-30) REVERT: A 511 ASP cc_start: 0.9037 (p0) cc_final: 0.8820 (p0) REVERT: B 470 MET cc_start: 0.8234 (mtm) cc_final: 0.7937 (mtt) REVERT: B 503 LYS cc_start: 0.9222 (ttmt) cc_final: 0.8926 (tptt) REVERT: C 440 ILE cc_start: 0.8193 (mt) cc_final: 0.7930 (mt) REVERT: C 441 GLN cc_start: 0.8282 (mm110) cc_final: 0.7993 (mm110) REVERT: C 447 ILE cc_start: 0.7512 (mt) cc_final: 0.7261 (mt) REVERT: C 461 ASP cc_start: 0.8728 (m-30) cc_final: 0.7446 (m-30) REVERT: D 450 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7705 (mt0) REVERT: D 470 MET cc_start: 0.8125 (ptp) cc_final: 0.7778 (ptt) REVERT: D 475 GLU cc_start: 0.9148 (tp30) cc_final: 0.8828 (tm-30) REVERT: D 483 ARG cc_start: 0.7984 (mtt180) cc_final: 0.6971 (ttp80) REVERT: D 507 GLN cc_start: 0.9115 (tm-30) cc_final: 0.8690 (tp-100) REVERT: D 513 LYS cc_start: 0.8662 (pptt) cc_final: 0.8412 (mmmt) REVERT: E 441 GLN cc_start: 0.9120 (mt0) cc_final: 0.8880 (mt0) REVERT: E 446 ASP cc_start: 0.9009 (m-30) cc_final: 0.8736 (m-30) REVERT: E 461 ASP cc_start: 0.8960 (m-30) cc_final: 0.8710 (m-30) REVERT: E 470 MET cc_start: 0.7501 (ptp) cc_final: 0.6940 (ptp) REVERT: E 473 ASP cc_start: 0.7764 (m-30) cc_final: 0.6995 (m-30) REVERT: E 483 ARG cc_start: 0.8091 (mtt180) cc_final: 0.7298 (ttm-80) REVERT: E 494 THR cc_start: 0.8802 (m) cc_final: 0.8576 (m) REVERT: E 497 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.7113 (mm-40) REVERT: F 460 LEU cc_start: 0.7365 (mt) cc_final: 0.7148 (mt) REVERT: F 515 MET cc_start: 0.7124 (tpt) cc_final: 0.6889 (tpt) REVERT: G 449 ASN cc_start: 0.8042 (t0) cc_final: 0.7730 (t0) REVERT: G 475 GLU cc_start: 0.7713 (mp0) cc_final: 0.6747 (pt0) REVERT: H 470 MET cc_start: 0.7717 (mpp) cc_final: 0.6908 (mpp) REVERT: H 477 VAL cc_start: 0.7488 (t) cc_final: 0.7239 (p) REVERT: H 486 LYS cc_start: 0.8311 (mtpt) cc_final: 0.7789 (ttmm) REVERT: I 476 LEU cc_start: 0.9234 (mt) cc_final: 0.8765 (mt) REVERT: I 477 VAL cc_start: 0.7254 (t) cc_final: 0.5689 (m) REVERT: I 482 THR cc_start: 0.8750 (p) cc_final: 0.8452 (p) REVERT: J 435 ILE cc_start: 0.7899 (mt) cc_final: 0.7691 (mt) REVERT: J 445 GLU cc_start: 0.7861 (mp0) cc_final: 0.7130 (mp0) REVERT: J 448 VAL cc_start: 0.8927 (t) cc_final: 0.8687 (m) REVERT: J 449 ASN cc_start: 0.9081 (m-40) cc_final: 0.8751 (m-40) REVERT: J 452 THR cc_start: 0.9191 (p) cc_final: 0.8496 (t) REVERT: J 467 ASP cc_start: 0.8304 (m-30) cc_final: 0.8080 (m-30) REVERT: J 470 MET cc_start: 0.7454 (mtm) cc_final: 0.7000 (mtm) REVERT: J 480 LYS cc_start: 0.8067 (pttm) cc_final: 0.7767 (pttm) REVERT: K 444 ARG cc_start: 0.6258 (ttm170) cc_final: 0.5612 (pmt170) REVERT: K 480 LYS cc_start: 0.7249 (mmtt) cc_final: 0.6910 (mmtt) REVERT: L 441 GLN cc_start: 0.9178 (mt0) cc_final: 0.8528 (tm-30) REVERT: L 453 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8019 (tm-30) REVERT: L 486 LYS cc_start: 0.9102 (ttmm) cc_final: 0.8609 (ttmm) REVERT: L 500 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8780 (mm-30) outliers start: 3 outliers final: 0 residues processed: 399 average time/residue: 0.1138 time to fit residues: 59.1356 Evaluate side-chains 293 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 292 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 84 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 8 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 458 GLN A 512 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN C 497 GLN D 458 GLN E 497 GLN ** F 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 ASN H 450 GLN H 512 ASN ** I 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN L 512 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.075471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.061229 restraints weight = 35422.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.063389 restraints weight = 23815.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.065059 restraints weight = 17527.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.066313 restraints weight = 13643.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.067308 restraints weight = 11102.839| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 1.5270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 8328 Z= 0.230 Angle : 0.805 9.650 11184 Z= 0.437 Chirality : 0.046 0.194 1332 Planarity : 0.006 0.072 1440 Dihedral : 5.827 24.944 1092 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.65 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % 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 are not related in a simple way. whole: -0.84 (0.24), residues: 1020 helix: -0.37 (0.16), residues: 852 sheet: None (None), residues: 0 loop : -0.63 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 483 TYR 0.015 0.002 TYR F 474 PHE 0.032 0.003 PHE J 501 TRP 0.031 0.003 TRP K 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.23 ( 8328) covalent geometry : angle 0.80459 / 0.44 (11184) hydrogen bonds : bond 0.04583 / 3.03 ( 529) hydrogen bonds : angle 4.77425 / 3.52 ( 1587) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 462 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 THR cc_start: 0.7306 (m) cc_final: 0.6828 (p) REVERT: A 443 LYS cc_start: 0.8631 (ptmm) cc_final: 0.8296 (pmmt) REVERT: A 445 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8157 (pm20) REVERT: A 461 ASP cc_start: 0.8995 (m-30) cc_final: 0.8633 (m-30) REVERT: A 468 LEU cc_start: 0.9363 (mp) cc_final: 0.8974 (mm) REVERT: A 471 LYS cc_start: 0.9099 (ptpp) cc_final: 0.8845 (ptmm) REVERT: A 472 GLU cc_start: 0.9215 (mp0) cc_final: 0.8969 (mp0) REVERT: A 476 LEU cc_start: 0.9547 (mt) cc_final: 0.9286 (mt) REVERT: A 480 LYS cc_start: 0.9545 (mmtt) cc_final: 0.8975 (mmmt) REVERT: A 486 LYS cc_start: 0.9625 (mtpt) cc_final: 0.9321 (mtmm) REVERT: A 492 ASP cc_start: 0.9255 (m-30) cc_final: 0.8880 (m-30) REVERT: A 501 PHE cc_start: 0.9279 (t80) cc_final: 0.8954 (t80) REVERT: A 513 LYS cc_start: 0.9029 (mmpt) cc_final: 0.8792 (mmmt) REVERT: B 447 ILE cc_start: 0.8678 (mt) cc_final: 0.8414 (mt) REVERT: B 470 MET cc_start: 0.8694 (mtm) cc_final: 0.7695 (mtt) REVERT: B 488 ARG cc_start: 0.8097 (mmt180) cc_final: 0.7514 (ptp-170) REVERT: B 500 GLU cc_start: 0.8414 (tt0) cc_final: 0.8187 (pm20) REVERT: B 515 MET cc_start: 0.7173 (tmm) cc_final: 0.6421 (tmm) REVERT: C 456 LEU cc_start: 0.9434 (tp) cc_final: 0.9173 (tp) REVERT: C 470 MET cc_start: 0.8756 (mtm) cc_final: 0.8310 (mtm) REVERT: C 478 SER cc_start: 0.9564 (t) cc_final: 0.9267 (p) REVERT: C 480 LYS cc_start: 0.9390 (mmtm) cc_final: 0.9139 (mmtp) REVERT: C 486 LYS cc_start: 0.9515 (mttt) cc_final: 0.9258 (mttp) REVERT: C 491 LEU cc_start: 0.8956 (mp) cc_final: 0.8551 (tt) REVERT: D 440 ILE cc_start: 0.9598 (tt) cc_final: 0.9325 (tt) REVERT: D 441 GLN cc_start: 0.8699 (tp-100) cc_final: 0.7825 (tp-100) REVERT: D 471 LYS cc_start: 0.9354 (tptp) cc_final: 0.9144 (tmtt) REVERT: D 483 ARG cc_start: 0.8744 (mtt180) cc_final: 0.8083 (ttp80) REVERT: D 493 THR cc_start: 0.8680 (m) cc_final: 0.8363 (p) REVERT: E 461 ASP cc_start: 0.8691 (m-30) cc_final: 0.7363 (t70) REVERT: E 470 MET cc_start: 0.8238 (ptp) cc_final: 0.7440 (ptp) REVERT: E 473 ASP cc_start: 0.8627 (m-30) cc_final: 0.8329 (m-30) REVERT: E 474 TYR cc_start: 0.9172 (t80) cc_final: 0.8929 (t80) REVERT: G 446 ASP cc_start: 0.8824 (m-30) cc_final: 0.8033 (m-30) REVERT: G 461 ASP cc_start: 0.8530 (m-30) cc_final: 0.8278 (m-30) REVERT: G 475 GLU cc_start: 0.8039 (mp0) cc_final: 0.7214 (tp30) REVERT: G 485 SER cc_start: 0.8364 (m) cc_final: 0.7899 (p) REVERT: G 497 GLN cc_start: 0.4261 (mm-40) cc_final: 0.4046 (tp40) REVERT: H 441 GLN cc_start: 0.8974 (mt0) cc_final: 0.8201 (mm110) REVERT: H 443 LYS cc_start: 0.9186 (mttt) cc_final: 0.8753 (mtmm) REVERT: H 446 ASP cc_start: 0.8601 (m-30) cc_final: 0.8370 (m-30) REVERT: H 470 MET cc_start: 0.8734 (mpp) cc_final: 0.7325 (mpp) REVERT: H 485 SER cc_start: 0.9423 (m) cc_final: 0.9072 (p) REVERT: H 486 LYS cc_start: 0.9328 (mtpt) cc_final: 0.9102 (mtpp) REVERT: H 488 ARG cc_start: 0.8125 (mmt90) cc_final: 0.7645 (mmt180) REVERT: H 496 ILE cc_start: 0.6492 (tp) cc_final: 0.6209 (tp) REVERT: H 501 PHE cc_start: 0.8230 (t80) cc_final: 0.7798 (t80) REVERT: H 515 MET cc_start: 0.2834 (mmp) cc_final: 0.2000 (tpp) REVERT: I 461 ASP cc_start: 0.8704 (t70) cc_final: 0.8330 (t70) REVERT: I 475 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8421 (tt0) REVERT: I 482 THR cc_start: 0.9019 (p) cc_final: 0.8253 (p) REVERT: J 445 GLU cc_start: 0.8405 (mp0) cc_final: 0.7690 (mp0) REVERT: J 449 ASN cc_start: 0.9201 (m-40) cc_final: 0.8955 (m-40) REVERT: J 467 ASP cc_start: 0.8600 (m-30) cc_final: 0.7759 (m-30) REVERT: J 499 GLU cc_start: 0.8372 (pp20) cc_final: 0.7946 (tm-30) REVERT: J 503 LYS cc_start: 0.9115 (pptt) cc_final: 0.8893 (ptpp) REVERT: K 444 ARG cc_start: 0.6963 (ttm170) cc_final: 0.6408 (ptt-90) REVERT: K 449 ASN cc_start: 0.9295 (m110) cc_final: 0.8905 (m-40) REVERT: K 450 GLN cc_start: 0.8955 (mm-40) cc_final: 0.8676 (mt0) REVERT: K 486 LYS cc_start: 0.8696 (mtpt) cc_final: 0.8419 (mttp) REVERT: L 441 GLN cc_start: 0.9110 (mt0) cc_final: 0.8806 (tt0) REVERT: L 443 LYS cc_start: 0.9139 (mppt) cc_final: 0.8918 (ptpp) REVERT: L 451 MET cc_start: 0.8563 (tpt) cc_final: 0.8327 (tpp) REVERT: L 492 ASP cc_start: 0.9246 (m-30) cc_final: 0.8997 (m-30) REVERT: L 503 LYS cc_start: 0.9321 (mtpp) cc_final: 0.8980 (mtpp) outliers start: 0 outliers final: 0 residues processed: 462 average time/residue: 0.1095 time to fit residues: 66.2732 Evaluate side-chains 355 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 72 optimal weight: 20.0000 chunk 37 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 95 optimal weight: 0.0970 chunk 87 optimal weight: 4.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 458 GLN A 512 ASN ** D 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 GLN E 438 GLN F 450 GLN F 458 GLN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 ASN H 514 GLN ** I 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 497 GLN ** J 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN L 512 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.073306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.058877 restraints weight = 36172.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.060901 restraints weight = 24287.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.062487 restraints weight = 18121.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.063654 restraints weight = 14263.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.064574 restraints weight = 11831.323| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 1.6326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8328 Z= 0.158 Angle : 0.704 6.647 11184 Z= 0.384 Chirality : 0.043 0.162 1332 Planarity : 0.005 0.070 1440 Dihedral : 5.387 22.679 1092 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.32 % Allowed : 2.32 % Favored : 97.36 % 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 are not related in a simple way. whole: -0.24 (0.24), residues: 1020 helix: 0.04 (0.17), residues: 852 sheet: None (None), residues: 0 loop : -0.47 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 444 TYR 0.026 0.002 TYR H 474 PHE 0.017 0.002 PHE J 501 TRP 0.033 0.003 TRP I 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 8328) covalent geometry : angle 0.70445 / 0.38 (11184) hydrogen bonds : bond 0.03803 / 2.47 ( 529) hydrogen bonds : angle 4.33042 / 3.19 ( 1587) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 459 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 GLN cc_start: 0.8972 (mt0) cc_final: 0.8194 (pp30) REVERT: A 461 ASP cc_start: 0.8908 (m-30) cc_final: 0.8347 (t70) REVERT: A 471 LYS cc_start: 0.9076 (ptpp) cc_final: 0.8568 (ptmm) REVERT: A 476 LEU cc_start: 0.9674 (mt) cc_final: 0.9452 (mt) REVERT: A 480 LYS cc_start: 0.9539 (mmtt) cc_final: 0.9140 (mmmt) REVERT: A 486 LYS cc_start: 0.9560 (mtpt) cc_final: 0.9310 (mtmm) REVERT: A 488 ARG cc_start: 0.8401 (ttm-80) cc_final: 0.8155 (ttm-80) REVERT: A 489 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7958 (tm-30) REVERT: A 492 ASP cc_start: 0.9258 (m-30) cc_final: 0.8859 (m-30) REVERT: A 513 LYS cc_start: 0.9056 (mmpt) cc_final: 0.8834 (mmmt) REVERT: B 441 GLN cc_start: 0.8496 (mm110) cc_final: 0.8287 (mm110) REVERT: B 476 LEU cc_start: 0.9446 (mt) cc_final: 0.9176 (mt) REVERT: B 484 THR cc_start: 0.8372 (p) cc_final: 0.7690 (p) REVERT: B 488 ARG cc_start: 0.7777 (mmt180) cc_final: 0.7548 (ptp-170) REVERT: B 495 ASP cc_start: 0.7944 (t0) cc_final: 0.7689 (t0) REVERT: C 441 GLN cc_start: 0.8512 (mm110) cc_final: 0.8025 (tp-100) REVERT: C 456 LEU cc_start: 0.9554 (tp) cc_final: 0.9258 (tp) REVERT: C 459 SER cc_start: 0.9715 (m) cc_final: 0.9379 (p) REVERT: C 480 LYS cc_start: 0.9326 (mmtm) cc_final: 0.9023 (mmtp) REVERT: C 486 LYS cc_start: 0.9523 (mttt) cc_final: 0.9261 (mttp) REVERT: C 489 GLN cc_start: 0.7900 (mp10) cc_final: 0.7524 (mp10) REVERT: C 491 LEU cc_start: 0.9107 (mp) cc_final: 0.8482 (tt) REVERT: C 492 ASP cc_start: 0.9176 (m-30) cc_final: 0.8938 (m-30) REVERT: D 441 GLN cc_start: 0.8368 (tp-100) cc_final: 0.8077 (tp-100) REVERT: D 446 ASP cc_start: 0.9059 (m-30) cc_final: 0.8785 (m-30) REVERT: D 450 GLN cc_start: 0.8442 (mm110) cc_final: 0.8172 (mm-40) REVERT: D 458 GLN cc_start: 0.8674 (mp10) cc_final: 0.8433 (pt0) REVERT: D 468 LEU cc_start: 0.9216 (mp) cc_final: 0.9001 (mt) REVERT: D 474 TYR cc_start: 0.9527 (t80) cc_final: 0.9072 (t80) REVERT: D 483 ARG cc_start: 0.8814 (mtt180) cc_final: 0.8401 (ttp80) REVERT: D 507 GLN cc_start: 0.9218 (tm-30) cc_final: 0.8756 (tp-100) REVERT: E 438 GLN cc_start: 0.9265 (OUTLIER) cc_final: 0.9039 (pp30) REVERT: E 461 ASP cc_start: 0.8817 (m-30) cc_final: 0.7310 (t70) REVERT: E 470 MET cc_start: 0.8518 (ptp) cc_final: 0.7621 (ptp) REVERT: E 471 LYS cc_start: 0.8670 (tttt) cc_final: 0.8309 (pttt) REVERT: E 473 ASP cc_start: 0.8808 (m-30) cc_final: 0.8431 (m-30) REVERT: E 483 ARG cc_start: 0.8513 (ttt180) cc_final: 0.8189 (ttt90) REVERT: E 489 GLN cc_start: 0.8541 (mp10) cc_final: 0.8223 (mp10) REVERT: F 450 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8331 (tp40) REVERT: G 446 ASP cc_start: 0.8730 (m-30) cc_final: 0.7833 (m-30) REVERT: G 461 ASP cc_start: 0.8928 (m-30) cc_final: 0.8662 (t0) REVERT: G 467 ASP cc_start: 0.8592 (t70) cc_final: 0.8346 (t70) REVERT: G 470 MET cc_start: -0.1434 (ptt) cc_final: -0.1650 (ptt) REVERT: G 475 GLU cc_start: 0.7997 (mp0) cc_final: 0.7000 (tm-30) REVERT: G 485 SER cc_start: 0.8183 (m) cc_final: 0.7141 (m) REVERT: G 506 VAL cc_start: 0.9377 (t) cc_final: 0.8991 (t) REVERT: H 470 MET cc_start: 0.8864 (mpp) cc_final: 0.7870 (mpp) REVERT: H 486 LYS cc_start: 0.9178 (mtpt) cc_final: 0.8898 (mttm) REVERT: H 500 GLU cc_start: 0.7808 (mp0) cc_final: 0.7494 (pm20) REVERT: H 501 PHE cc_start: 0.8616 (t80) cc_final: 0.8096 (t80) REVERT: H 504 VAL cc_start: 0.9305 (p) cc_final: 0.9077 (m) REVERT: H 515 MET cc_start: 0.3277 (mmp) cc_final: 0.2644 (mmp) REVERT: I 474 TYR cc_start: 0.8913 (t80) cc_final: 0.8649 (t80) REVERT: I 475 GLU cc_start: 0.9254 (mm-30) cc_final: 0.8889 (mt-10) REVERT: I 491 LEU cc_start: 0.8631 (mp) cc_final: 0.8246 (mt) REVERT: I 515 MET cc_start: 0.6267 (tpt) cc_final: 0.5497 (tpp) REVERT: J 430 THR cc_start: 0.7667 (m) cc_final: 0.7404 (t) REVERT: J 445 GLU cc_start: 0.8510 (mp0) cc_final: 0.8155 (mp0) REVERT: J 449 ASN cc_start: 0.9293 (m-40) cc_final: 0.9033 (m-40) REVERT: J 451 MET cc_start: 0.9177 (tpp) cc_final: 0.8907 (tpp) REVERT: J 453 GLU cc_start: 0.9373 (tp30) cc_final: 0.8933 (tp30) REVERT: J 469 ILE cc_start: 0.9127 (tt) cc_final: 0.8867 (tt) REVERT: J 470 MET cc_start: 0.9203 (mtm) cc_final: 0.8699 (mtt) REVERT: J 471 LYS cc_start: 0.9348 (mmtm) cc_final: 0.9136 (pttt) REVERT: J 500 GLU cc_start: 0.9161 (tp30) cc_final: 0.8818 (tp30) REVERT: K 444 ARG cc_start: 0.6844 (ttm170) cc_final: 0.6207 (ptt-90) REVERT: K 449 ASN cc_start: 0.9232 (m110) cc_final: 0.8847 (m110) REVERT: K 450 GLN cc_start: 0.8850 (mm-40) cc_final: 0.8612 (mt0) REVERT: K 456 LEU cc_start: 0.9199 (tp) cc_final: 0.8792 (tp) REVERT: K 460 LEU cc_start: 0.9515 (mt) cc_final: 0.9313 (mt) REVERT: K 486 LYS cc_start: 0.8810 (mtpt) cc_final: 0.8277 (mttp) REVERT: K 509 LEU cc_start: 0.9084 (mt) cc_final: 0.8835 (mt) REVERT: L 437 GLN cc_start: 0.9414 (pt0) cc_final: 0.9075 (pm20) REVERT: L 441 GLN cc_start: 0.9177 (mt0) cc_final: 0.8714 (tm-30) REVERT: L 460 LEU cc_start: 0.9444 (mp) cc_final: 0.9159 (mp) REVERT: L 476 LEU cc_start: 0.9459 (mt) cc_final: 0.9202 (mt) REVERT: L 480 LYS cc_start: 0.7722 (pttm) cc_final: 0.6926 (pttt) REVERT: L 492 ASP cc_start: 0.9396 (m-30) cc_final: 0.9111 (m-30) REVERT: L 503 LYS cc_start: 0.9380 (mtpp) cc_final: 0.9170 (mtpp) outliers start: 3 outliers final: 0 residues processed: 461 average time/residue: 0.1064 time to fit residues: 64.9901 Evaluate side-chains 372 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 370 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 13 optimal weight: 0.0980 chunk 46 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 458 GLN A 512 ASN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN F 441 GLN ** F 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 512 ASN ** I 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 449 ASN L 512 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.067395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.054007 restraints weight = 37285.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.055982 restraints weight = 24460.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.057490 restraints weight = 17957.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.058575 restraints weight = 14032.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.059449 restraints weight = 11572.709| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 1.8140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8328 Z= 0.211 Angle : 0.782 8.071 11184 Z= 0.428 Chirality : 0.045 0.190 1332 Planarity : 0.005 0.075 1440 Dihedral : 5.668 23.783 1092 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.24), residues: 1020 helix: -0.12 (0.16), residues: 852 sheet: None (None), residues: 0 loop : -0.73 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 466 TYR 0.016 0.002 TYR J 474 PHE 0.021 0.003 PHE J 501 TRP 0.024 0.003 TRP I 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 ( 8328) covalent geometry : angle 0.78207 / 0.43 (11184) hydrogen bonds : bond 0.04173 / 2.73 ( 529) hydrogen bonds : angle 4.66288 / 3.39 ( 1587) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 474 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 ASP cc_start: 0.8847 (t0) cc_final: 0.8402 (t0) REVERT: A 461 ASP cc_start: 0.8986 (m-30) cc_final: 0.8383 (t70) REVERT: A 471 LYS cc_start: 0.9143 (ptpp) cc_final: 0.8433 (ptmm) REVERT: A 472 GLU cc_start: 0.9061 (mp0) cc_final: 0.8682 (mp0) REVERT: A 480 LYS cc_start: 0.9580 (mmtt) cc_final: 0.9275 (mmmt) REVERT: A 489 GLN cc_start: 0.8219 (tm-30) cc_final: 0.7994 (tm-30) REVERT: A 492 ASP cc_start: 0.9277 (m-30) cc_final: 0.8950 (m-30) REVERT: A 495 ASP cc_start: 0.9289 (p0) cc_final: 0.8949 (p0) REVERT: A 501 PHE cc_start: 0.9263 (t80) cc_final: 0.8816 (t80) REVERT: A 513 LYS cc_start: 0.9006 (mmpt) cc_final: 0.8787 (mmmt) REVERT: B 449 ASN cc_start: 0.8067 (t0) cc_final: 0.7843 (t0) REVERT: B 470 MET cc_start: 0.8565 (mtt) cc_final: 0.8002 (mtp) REVERT: B 495 ASP cc_start: 0.7944 (t0) cc_final: 0.7562 (t0) REVERT: C 456 LEU cc_start: 0.9680 (tp) cc_final: 0.9404 (tp) REVERT: C 461 ASP cc_start: 0.9030 (m-30) cc_final: 0.8669 (m-30) REVERT: C 470 MET cc_start: 0.8675 (mtp) cc_final: 0.8349 (mtm) REVERT: C 471 LYS cc_start: 0.9264 (tmmt) cc_final: 0.8966 (tmtt) REVERT: C 479 THR cc_start: 0.8924 (m) cc_final: 0.8718 (p) REVERT: C 480 LYS cc_start: 0.9334 (mmtm) cc_final: 0.9014 (mmtp) REVERT: C 486 LYS cc_start: 0.9496 (mttt) cc_final: 0.9122 (mttp) REVERT: C 489 GLN cc_start: 0.7714 (mp10) cc_final: 0.7472 (mp10) REVERT: C 491 LEU cc_start: 0.9230 (mp) cc_final: 0.8197 (tt) REVERT: D 441 GLN cc_start: 0.8621 (tp-100) cc_final: 0.8169 (tp-100) REVERT: D 450 GLN cc_start: 0.8444 (mm110) cc_final: 0.8241 (mm-40) REVERT: D 477 VAL cc_start: 0.9244 (t) cc_final: 0.9015 (t) REVERT: D 480 LYS cc_start: 0.9090 (mmmm) cc_final: 0.8715 (mmmm) REVERT: E 441 GLN cc_start: 0.9084 (mt0) cc_final: 0.8820 (mp10) REVERT: E 443 LYS cc_start: 0.9464 (ptpt) cc_final: 0.8294 (ptpp) REVERT: E 446 ASP cc_start: 0.9388 (m-30) cc_final: 0.8888 (p0) REVERT: E 461 ASP cc_start: 0.8781 (m-30) cc_final: 0.7249 (t70) REVERT: E 503 LYS cc_start: 0.9408 (pttm) cc_final: 0.9184 (pttm) REVERT: F 447 ILE cc_start: 0.9221 (mt) cc_final: 0.8994 (mt) REVERT: F 461 ASP cc_start: 0.9394 (t70) cc_final: 0.8154 (t70) REVERT: G 446 ASP cc_start: 0.8824 (m-30) cc_final: 0.7881 (m-30) REVERT: G 475 GLU cc_start: 0.7908 (mp0) cc_final: 0.7100 (tm-30) REVERT: G 500 GLU cc_start: 0.7527 (pm20) cc_final: 0.7226 (pm20) REVERT: H 446 ASP cc_start: 0.9163 (m-30) cc_final: 0.8958 (m-30) REVERT: H 470 MET cc_start: 0.8571 (mpp) cc_final: 0.7479 (mtm) REVERT: H 473 ASP cc_start: 0.8783 (m-30) cc_final: 0.8550 (m-30) REVERT: H 489 GLN cc_start: 0.8395 (tt0) cc_final: 0.8120 (tt0) REVERT: H 496 ILE cc_start: 0.8011 (tp) cc_final: 0.7796 (tp) REVERT: H 500 GLU cc_start: 0.8078 (mp0) cc_final: 0.7742 (pm20) REVERT: H 501 PHE cc_start: 0.8615 (t80) cc_final: 0.8069 (t80) REVERT: I 445 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8667 (mp0) REVERT: I 449 ASN cc_start: 0.8933 (m110) cc_final: 0.8639 (m-40) REVERT: I 461 ASP cc_start: 0.8822 (t70) cc_final: 0.7751 (t70) REVERT: I 475 GLU cc_start: 0.9297 (mm-30) cc_final: 0.9082 (mt-10) REVERT: I 478 SER cc_start: 0.9659 (t) cc_final: 0.9420 (p) REVERT: I 484 THR cc_start: 0.9261 (p) cc_final: 0.8737 (p) REVERT: I 488 ARG cc_start: 0.7783 (mtt-85) cc_final: 0.7324 (mtp85) REVERT: I 515 MET cc_start: 0.6650 (tpt) cc_final: 0.5647 (tpp) REVERT: J 445 GLU cc_start: 0.8777 (mp0) cc_final: 0.8296 (mp0) REVERT: J 446 ASP cc_start: 0.8629 (t70) cc_final: 0.8257 (t0) REVERT: J 449 ASN cc_start: 0.9309 (m-40) cc_final: 0.8985 (m-40) REVERT: J 450 GLN cc_start: 0.8992 (mt0) cc_final: 0.8708 (mm-40) REVERT: J 451 MET cc_start: 0.9464 (tpp) cc_final: 0.9189 (tpp) REVERT: J 453 GLU cc_start: 0.9374 (tp30) cc_final: 0.8791 (tp30) REVERT: J 457 ASN cc_start: 0.9042 (p0) cc_final: 0.8753 (p0) REVERT: J 469 ILE cc_start: 0.9097 (tt) cc_final: 0.8801 (tt) REVERT: J 470 MET cc_start: 0.9238 (mtm) cc_final: 0.8117 (mtt) REVERT: J 471 LYS cc_start: 0.9406 (mmtm) cc_final: 0.9070 (pttt) REVERT: J 475 GLU cc_start: 0.9256 (mt-10) cc_final: 0.9039 (mt-10) REVERT: J 489 GLN cc_start: 0.9083 (tm-30) cc_final: 0.8795 (tm-30) REVERT: J 495 ASP cc_start: 0.9397 (m-30) cc_final: 0.9140 (m-30) REVERT: J 501 PHE cc_start: 0.9192 (t80) cc_final: 0.8818 (t80) REVERT: K 444 ARG cc_start: 0.7277 (ttm170) cc_final: 0.6615 (ptt180) REVERT: K 449 ASN cc_start: 0.9297 (m110) cc_final: 0.9076 (m-40) REVERT: K 456 LEU cc_start: 0.9530 (tp) cc_final: 0.9294 (tp) REVERT: K 476 LEU cc_start: 0.9433 (mt) cc_final: 0.9204 (mt) REVERT: K 486 LYS cc_start: 0.9326 (mtpt) cc_final: 0.8540 (mtpt) REVERT: K 489 GLN cc_start: 0.8883 (tm-30) cc_final: 0.8486 (tm-30) REVERT: L 437 GLN cc_start: 0.9406 (pt0) cc_final: 0.9032 (pm20) REVERT: L 441 GLN cc_start: 0.9215 (mt0) cc_final: 0.8956 (tm-30) REVERT: L 460 LEU cc_start: 0.9529 (mp) cc_final: 0.9156 (mp) REVERT: L 472 GLU cc_start: 0.7093 (tt0) cc_final: 0.6859 (tt0) REVERT: L 476 LEU cc_start: 0.9434 (mt) cc_final: 0.9184 (mt) REVERT: L 492 ASP cc_start: 0.9369 (m-30) cc_final: 0.8992 (m-30) REVERT: L 503 LYS cc_start: 0.9393 (mtpp) cc_final: 0.9156 (mtpp) outliers start: 0 outliers final: 0 residues processed: 474 average time/residue: 0.1067 time to fit residues: 66.9723 Evaluate side-chains 370 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 74 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 48 optimal weight: 20.0000 chunk 6 optimal weight: 0.2980 chunk 82 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 458 GLN A 512 ASN B 489 GLN ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 514 GLN ** H 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 512 ASN ** I 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 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** ** K 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN K 514 GLN L 512 ASN L 514 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.068890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.054809 restraints weight = 36540.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.056856 restraints weight = 24241.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.058396 restraints weight = 17835.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.059537 restraints weight = 13956.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.060451 restraints weight = 11500.650| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 1.8513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8328 Z= 0.151 Angle : 0.741 6.827 11184 Z= 0.401 Chirality : 0.044 0.166 1332 Planarity : 0.004 0.087 1440 Dihedral : 5.450 23.944 1092 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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 are not related in a simple way. whole: -0.33 (0.25), residues: 1020 helix: 0.03 (0.17), residues: 852 sheet: None (None), residues: 0 loop : -0.79 (0.47), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 466 TYR 0.017 0.001 TYR H 474 PHE 0.018 0.002 PHE J 501 TRP 0.035 0.003 TRP A 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 8328) covalent geometry : angle 0.74134 / 0.40 (11184) hydrogen bonds : bond 0.03610 / 2.33 ( 529) hydrogen bonds : angle 4.59562 / 3.45 ( 1587) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 476 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 ASP cc_start: 0.8704 (t0) cc_final: 0.8293 (t0) REVERT: A 450 GLN cc_start: 0.8674 (mt0) cc_final: 0.8245 (pt0) REVERT: A 461 ASP cc_start: 0.9013 (m-30) cc_final: 0.8320 (t70) REVERT: A 470 MET cc_start: 0.9169 (mtt) cc_final: 0.8307 (mtt) REVERT: A 471 LYS cc_start: 0.9201 (ptpp) cc_final: 0.8405 (ptmm) REVERT: A 472 GLU cc_start: 0.9045 (mp0) cc_final: 0.8545 (mp0) REVERT: A 476 LEU cc_start: 0.9673 (mt) cc_final: 0.9350 (mt) REVERT: A 480 LYS cc_start: 0.9572 (mmtt) cc_final: 0.9150 (mmmt) REVERT: A 486 LYS cc_start: 0.9554 (mttp) cc_final: 0.8920 (mptp) REVERT: A 489 GLN cc_start: 0.8306 (tm-30) cc_final: 0.7877 (tt0) REVERT: A 492 ASP cc_start: 0.9242 (m-30) cc_final: 0.8856 (m-30) REVERT: A 501 PHE cc_start: 0.9220 (t80) cc_final: 0.8920 (t80) REVERT: A 513 LYS cc_start: 0.9059 (mmpt) cc_final: 0.8832 (mmmt) REVERT: B 440 ILE cc_start: 0.8593 (mt) cc_final: 0.8144 (mt) REVERT: B 443 LYS cc_start: 0.8365 (tptp) cc_final: 0.8089 (tppt) REVERT: B 449 ASN cc_start: 0.7991 (t0) cc_final: 0.7756 (t0) REVERT: B 489 GLN cc_start: 0.8989 (mm110) cc_final: 0.8657 (mm-40) REVERT: C 441 GLN cc_start: 0.8146 (mm110) cc_final: 0.7896 (tp-100) REVERT: C 456 LEU cc_start: 0.9609 (tp) cc_final: 0.9252 (tp) REVERT: C 459 SER cc_start: 0.9801 (m) cc_final: 0.9396 (p) REVERT: C 461 ASP cc_start: 0.9135 (m-30) cc_final: 0.8795 (m-30) REVERT: C 470 MET cc_start: 0.8754 (mtp) cc_final: 0.5927 (mtm) REVERT: C 479 THR cc_start: 0.9033 (m) cc_final: 0.8830 (p) REVERT: C 480 LYS cc_start: 0.9373 (mmtm) cc_final: 0.9030 (mmtp) REVERT: C 486 LYS cc_start: 0.9453 (mttt) cc_final: 0.9154 (mttp) REVERT: C 491 LEU cc_start: 0.9074 (mp) cc_final: 0.8385 (tt) REVERT: D 441 GLN cc_start: 0.8475 (tp-100) cc_final: 0.8003 (tp-100) REVERT: D 449 ASN cc_start: 0.8571 (m110) cc_final: 0.8181 (m110) REVERT: D 459 SER cc_start: 0.9438 (m) cc_final: 0.9188 (p) REVERT: D 468 LEU cc_start: 0.9175 (mp) cc_final: 0.8899 (mt) REVERT: D 480 LYS cc_start: 0.9082 (mmmm) cc_final: 0.8733 (mmmm) REVERT: E 443 LYS cc_start: 0.9492 (ptpt) cc_final: 0.9142 (ptpp) REVERT: E 446 ASP cc_start: 0.9366 (m-30) cc_final: 0.9033 (m-30) REVERT: E 461 ASP cc_start: 0.8391 (m-30) cc_final: 0.7164 (t0) REVERT: E 474 TYR cc_start: 0.9365 (t80) cc_final: 0.9136 (t80) REVERT: E 476 LEU cc_start: 0.9155 (mt) cc_final: 0.8910 (mt) REVERT: E 489 GLN cc_start: 0.8504 (mp10) cc_final: 0.8088 (mp10) REVERT: E 501 PHE cc_start: 0.8823 (t80) cc_final: 0.8184 (t80) REVERT: E 503 LYS cc_start: 0.9451 (pttm) cc_final: 0.9192 (pttm) REVERT: F 441 GLN cc_start: 0.7934 (tp-100) cc_final: 0.7541 (tp40) REVERT: F 446 ASP cc_start: 0.9049 (t70) cc_final: 0.8741 (t0) REVERT: F 482 THR cc_start: 0.8373 (t) cc_final: 0.8098 (p) REVERT: G 446 ASP cc_start: 0.8692 (m-30) cc_final: 0.7997 (m-30) REVERT: G 475 GLU cc_start: 0.8041 (mp0) cc_final: 0.7375 (tm-30) REVERT: H 468 LEU cc_start: 0.9272 (mt) cc_final: 0.9053 (mt) REVERT: H 470 MET cc_start: 0.8497 (mpp) cc_final: 0.7605 (mtm) REVERT: H 492 ASP cc_start: 0.9063 (m-30) cc_final: 0.8794 (m-30) REVERT: H 496 ILE cc_start: 0.7766 (tp) cc_final: 0.7398 (tp) REVERT: H 501 PHE cc_start: 0.8618 (t80) cc_final: 0.8156 (t80) REVERT: I 458 GLN cc_start: 0.9350 (mt0) cc_final: 0.8647 (mt0) REVERT: I 461 ASP cc_start: 0.9004 (t70) cc_final: 0.8077 (t70) REVERT: I 463 LEU cc_start: 0.9367 (mt) cc_final: 0.9121 (mt) REVERT: I 484 THR cc_start: 0.9139 (p) cc_final: 0.8827 (p) REVERT: I 515 MET cc_start: 0.6579 (tpt) cc_final: 0.5705 (tpp) REVERT: J 441 GLN cc_start: 0.7831 (tm-30) cc_final: 0.7484 (tm-30) REVERT: J 445 GLU cc_start: 0.8724 (mp0) cc_final: 0.8356 (mp0) REVERT: J 449 ASN cc_start: 0.9271 (m-40) cc_final: 0.8975 (m-40) REVERT: J 451 MET cc_start: 0.9329 (tpp) cc_final: 0.9088 (tpp) REVERT: J 453 GLU cc_start: 0.9331 (tp30) cc_final: 0.8838 (tp30) REVERT: J 457 ASN cc_start: 0.8907 (p0) cc_final: 0.8594 (p0) REVERT: J 470 MET cc_start: 0.8990 (mtm) cc_final: 0.8734 (mtt) REVERT: J 471 LYS cc_start: 0.9379 (mptt) cc_final: 0.9158 (pttt) REVERT: J 475 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8915 (mt-10) REVERT: J 476 LEU cc_start: 0.9489 (mt) cc_final: 0.9277 (mt) REVERT: J 480 LYS cc_start: 0.8691 (ptpp) cc_final: 0.8340 (ptpp) REVERT: J 489 GLN cc_start: 0.9120 (tm-30) cc_final: 0.8808 (tm-30) REVERT: J 495 ASP cc_start: 0.9409 (m-30) cc_final: 0.9145 (m-30) REVERT: J 500 GLU cc_start: 0.9226 (tp30) cc_final: 0.9022 (tp30) REVERT: J 501 PHE cc_start: 0.9159 (t80) cc_final: 0.8914 (t80) REVERT: K 444 ARG cc_start: 0.7176 (ttm170) cc_final: 0.6228 (ptt180) REVERT: K 449 ASN cc_start: 0.9412 (m110) cc_final: 0.9067 (m-40) REVERT: K 456 LEU cc_start: 0.9578 (tp) cc_final: 0.9234 (tp) REVERT: K 476 LEU cc_start: 0.9381 (mt) cc_final: 0.9109 (mt) REVERT: K 486 LYS cc_start: 0.9355 (mtpt) cc_final: 0.9089 (mttm) REVERT: L 437 GLN cc_start: 0.9368 (pt0) cc_final: 0.9132 (pm20) REVERT: L 441 GLN cc_start: 0.9127 (mt0) cc_final: 0.8903 (tm-30) REVERT: L 460 LEU cc_start: 0.9468 (mp) cc_final: 0.9240 (mp) REVERT: L 476 LEU cc_start: 0.9452 (mt) cc_final: 0.9197 (mt) REVERT: L 492 ASP cc_start: 0.9318 (m-30) cc_final: 0.8874 (m-30) outliers start: 0 outliers final: 0 residues processed: 476 average time/residue: 0.1032 time to fit residues: 64.8486 Evaluate side-chains 386 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 386 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 87 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 GLN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 GLN ** F 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 512 ASN ** I 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 438 GLN ** K 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 512 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.066361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.052545 restraints weight = 37508.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.054454 restraints weight = 25010.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.055899 restraints weight = 18597.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.056994 restraints weight = 14680.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.057847 restraints weight = 12142.036| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 1.9173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8328 Z= 0.173 Angle : 0.774 7.534 11184 Z= 0.419 Chirality : 0.046 0.181 1332 Planarity : 0.005 0.074 1440 Dihedral : 5.410 26.230 1092 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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 are not related in a simple way. whole: -0.38 (0.25), residues: 1020 helix: 0.02 (0.17), residues: 852 sheet: None (None), residues: 0 loop : -0.92 (0.47), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 466 TYR 0.016 0.002 TYR K 474 PHE 0.016 0.003 PHE J 501 TRP 0.033 0.003 TRP I 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 ( 8328) covalent geometry : angle 0.77417 / 0.42 (11184) hydrogen bonds : bond 0.03713 / 2.41 ( 529) hydrogen bonds : angle 4.66834 / 3.48 ( 1587) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 468 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 ASP cc_start: 0.8814 (t0) cc_final: 0.8571 (t0) REVERT: A 450 GLN cc_start: 0.8682 (mt0) cc_final: 0.8415 (pt0) REVERT: A 461 ASP cc_start: 0.9035 (m-30) cc_final: 0.8362 (t70) REVERT: A 471 LYS cc_start: 0.9088 (ptpp) cc_final: 0.8470 (ptmm) REVERT: A 472 GLU cc_start: 0.9110 (mp0) cc_final: 0.8795 (mp0) REVERT: A 480 LYS cc_start: 0.9573 (mmtt) cc_final: 0.9298 (mmmt) REVERT: A 486 LYS cc_start: 0.9564 (mttp) cc_final: 0.8884 (mttp) REVERT: A 488 ARG cc_start: 0.8438 (ttm-80) cc_final: 0.8109 (ttm-80) REVERT: A 492 ASP cc_start: 0.9264 (m-30) cc_final: 0.8951 (m-30) REVERT: A 501 PHE cc_start: 0.9240 (t80) cc_final: 0.8794 (t80) REVERT: A 513 LYS cc_start: 0.9049 (mmpt) cc_final: 0.8821 (mmmt) REVERT: B 449 ASN cc_start: 0.8017 (t0) cc_final: 0.7802 (t0) REVERT: B 453 GLU cc_start: 0.9088 (tp30) cc_final: 0.8874 (tp30) REVERT: B 472 GLU cc_start: 0.8719 (pm20) cc_final: 0.8492 (pm20) REVERT: C 441 GLN cc_start: 0.8268 (mm110) cc_final: 0.8039 (tp-100) REVERT: C 445 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8730 (mt-10) REVERT: C 450 GLN cc_start: 0.7630 (mt0) cc_final: 0.7251 (tt0) REVERT: C 456 LEU cc_start: 0.9617 (tp) cc_final: 0.9263 (tp) REVERT: C 459 SER cc_start: 0.9810 (m) cc_final: 0.9413 (p) REVERT: C 461 ASP cc_start: 0.9134 (m-30) cc_final: 0.8765 (m-30) REVERT: C 468 LEU cc_start: 0.9332 (mp) cc_final: 0.8972 (mm) REVERT: C 470 MET cc_start: 0.8647 (mtp) cc_final: 0.6416 (mtm) REVERT: C 480 LYS cc_start: 0.9348 (mmtm) cc_final: 0.8907 (mmtp) REVERT: C 486 LYS cc_start: 0.9455 (mttt) cc_final: 0.9059 (mttp) REVERT: D 441 GLN cc_start: 0.8581 (tp-100) cc_final: 0.8164 (tp-100) REVERT: D 480 LYS cc_start: 0.9123 (mmmm) cc_final: 0.8790 (mmmm) REVERT: D 503 LYS cc_start: 0.8953 (pttm) cc_final: 0.8735 (pttm) REVERT: E 443 LYS cc_start: 0.9554 (ptpt) cc_final: 0.9256 (ptpp) REVERT: E 461 ASP cc_start: 0.8861 (m-30) cc_final: 0.7225 (t0) REVERT: E 474 TYR cc_start: 0.9389 (t80) cc_final: 0.9061 (t80) REVERT: E 486 LYS cc_start: 0.9258 (mttt) cc_final: 0.9054 (mttm) REVERT: E 489 GLN cc_start: 0.8471 (mp10) cc_final: 0.8202 (mp10) REVERT: E 496 ILE cc_start: 0.8658 (pt) cc_final: 0.8450 (mp) REVERT: E 501 PHE cc_start: 0.8843 (t80) cc_final: 0.8216 (t80) REVERT: E 503 LYS cc_start: 0.9397 (pttm) cc_final: 0.9083 (pttm) REVERT: F 441 GLN cc_start: 0.8301 (tp-100) cc_final: 0.7888 (tp40) REVERT: F 446 ASP cc_start: 0.9118 (t70) cc_final: 0.8852 (t0) REVERT: F 461 ASP cc_start: 0.9404 (t70) cc_final: 0.7829 (t70) REVERT: F 482 THR cc_start: 0.8485 (t) cc_final: 0.8161 (p) REVERT: F 515 MET cc_start: 0.6899 (tpt) cc_final: 0.6632 (tpp) REVERT: G 446 ASP cc_start: 0.8720 (m-30) cc_final: 0.8109 (m-30) REVERT: G 453 GLU cc_start: 0.8925 (mp0) cc_final: 0.8690 (mp0) REVERT: G 475 GLU cc_start: 0.8283 (mp0) cc_final: 0.7374 (tm-30) REVERT: G 515 MET cc_start: 0.2617 (mmp) cc_final: 0.2303 (mmp) REVERT: H 470 MET cc_start: 0.8811 (mpp) cc_final: 0.7428 (mtt) REVERT: H 480 LYS cc_start: 0.8536 (ptpp) cc_final: 0.7189 (ptpt) REVERT: H 486 LYS cc_start: 0.9468 (mttm) cc_final: 0.9036 (mttm) REVERT: H 488 ARG cc_start: 0.8476 (mmm-85) cc_final: 0.8214 (mmm-85) REVERT: H 500 GLU cc_start: 0.8271 (mp0) cc_final: 0.7981 (pm20) REVERT: H 501 PHE cc_start: 0.8705 (t80) cc_final: 0.8234 (t80) REVERT: I 463 LEU cc_start: 0.9437 (mt) cc_final: 0.9197 (mt) REVERT: I 515 MET cc_start: 0.6682 (tpt) cc_final: 0.5787 (tpp) REVERT: J 445 GLU cc_start: 0.8924 (mp0) cc_final: 0.8327 (mp0) REVERT: J 449 ASN cc_start: 0.9140 (m-40) cc_final: 0.8801 (m-40) REVERT: J 451 MET cc_start: 0.9270 (tpp) cc_final: 0.9035 (tpp) REVERT: J 453 GLU cc_start: 0.9376 (tp30) cc_final: 0.8856 (tp30) REVERT: J 457 ASN cc_start: 0.8880 (p0) cc_final: 0.8656 (p0) REVERT: J 470 MET cc_start: 0.9018 (mtm) cc_final: 0.8724 (mtt) REVERT: J 489 GLN cc_start: 0.9195 (tm-30) cc_final: 0.8895 (tm-30) REVERT: J 495 ASP cc_start: 0.9459 (m-30) cc_final: 0.9198 (m-30) REVERT: K 444 ARG cc_start: 0.7352 (ttm170) cc_final: 0.6525 (ptt180) REVERT: K 449 ASN cc_start: 0.9390 (m110) cc_final: 0.9081 (m-40) REVERT: K 452 THR cc_start: 0.9050 (p) cc_final: 0.8774 (p) REVERT: K 456 LEU cc_start: 0.9665 (tp) cc_final: 0.9412 (tp) REVERT: K 471 LYS cc_start: 0.8984 (mmmm) cc_final: 0.8445 (mtpp) REVERT: K 476 LEU cc_start: 0.9503 (mt) cc_final: 0.9263 (mt) REVERT: K 486 LYS cc_start: 0.9364 (mtpt) cc_final: 0.9117 (mtpp) REVERT: L 437 GLN cc_start: 0.9359 (pt0) cc_final: 0.8717 (pm20) REVERT: L 440 ILE cc_start: 0.9733 (mm) cc_final: 0.9447 (mm) REVERT: L 441 GLN cc_start: 0.9160 (mt0) cc_final: 0.8864 (mm-40) REVERT: L 460 LEU cc_start: 0.9492 (mp) cc_final: 0.9187 (mp) REVERT: L 476 LEU cc_start: 0.9475 (mt) cc_final: 0.9241 (mt) REVERT: L 480 LYS cc_start: 0.7404 (pttm) cc_final: 0.7096 (pttm) REVERT: L 492 ASP cc_start: 0.9303 (m-30) cc_final: 0.8932 (m-30) REVERT: L 503 LYS cc_start: 0.9388 (mtpp) cc_final: 0.9068 (mtpp) outliers start: 0 outliers final: 0 residues processed: 468 average time/residue: 0.0957 time to fit residues: 60.1702 Evaluate side-chains 387 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 19 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 32 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 43 optimal weight: 0.1980 chunk 48 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 458 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** C 458 GLN D 458 GLN D 497 GLN ** E 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 438 GLN F 449 ASN ** F 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 497 GLN ** H 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 512 ASN ** I 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN L 512 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.062790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.049554 restraints weight = 38689.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.051395 restraints weight = 25466.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.052739 restraints weight = 18817.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.053772 restraints weight = 14849.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.054550 restraints weight = 12340.226| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 2.0322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8328 Z= 0.211 Angle : 0.829 7.445 11184 Z= 0.447 Chirality : 0.049 0.188 1332 Planarity : 0.006 0.077 1440 Dihedral : 5.767 27.789 1092 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 21.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.12 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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 are not related in a simple way. whole: -0.77 (0.25), residues: 1020 helix: -0.24 (0.17), residues: 852 sheet: None (None), residues: 0 loop : -1.17 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 466 TYR 0.016 0.002 TYR J 474 PHE 0.026 0.003 PHE J 501 TRP 0.037 0.003 TRP I 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 ( 8328) covalent geometry : angle 0.82929 / 0.45 (11184) hydrogen bonds : bond 0.04033 / 2.58 ( 529) hydrogen bonds : angle 4.95927 / 3.70 ( 1587) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 464 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 GLN cc_start: 0.8670 (mt0) cc_final: 0.8324 (pt0) REVERT: A 461 ASP cc_start: 0.9054 (m-30) cc_final: 0.8738 (t70) REVERT: A 470 MET cc_start: 0.9041 (mtt) cc_final: 0.8836 (mtt) REVERT: A 480 LYS cc_start: 0.9489 (mmtt) cc_final: 0.9173 (mmmm) REVERT: A 488 ARG cc_start: 0.8377 (ttm-80) cc_final: 0.8010 (ttm-80) REVERT: A 492 ASP cc_start: 0.9081 (m-30) cc_final: 0.8803 (m-30) REVERT: A 501 PHE cc_start: 0.9305 (t80) cc_final: 0.8782 (t80) REVERT: B 445 GLU cc_start: 0.8494 (tp30) cc_final: 0.8249 (tp30) REVERT: B 472 GLU cc_start: 0.8692 (pm20) cc_final: 0.8478 (pm20) REVERT: B 492 ASP cc_start: 0.9289 (m-30) cc_final: 0.9078 (m-30) REVERT: C 443 LYS cc_start: 0.8966 (pttp) cc_final: 0.8757 (pttp) REVERT: C 447 ILE cc_start: 0.8702 (mp) cc_final: 0.8499 (mp) REVERT: C 450 GLN cc_start: 0.7989 (mt0) cc_final: 0.6847 (tm-30) REVERT: C 456 LEU cc_start: 0.9652 (tp) cc_final: 0.9378 (tp) REVERT: C 461 ASP cc_start: 0.8994 (m-30) cc_final: 0.8557 (m-30) REVERT: C 470 MET cc_start: 0.8191 (mtp) cc_final: 0.7959 (mtm) REVERT: C 473 ASP cc_start: 0.9485 (m-30) cc_final: 0.9277 (m-30) REVERT: C 480 LYS cc_start: 0.9355 (mmtm) cc_final: 0.9118 (mmtp) REVERT: C 486 LYS cc_start: 0.9447 (mttt) cc_final: 0.9107 (mttp) REVERT: D 441 GLN cc_start: 0.8610 (tp-100) cc_final: 0.8209 (tp-100) REVERT: D 449 ASN cc_start: 0.8908 (m110) cc_final: 0.8617 (m-40) REVERT: D 464 LEU cc_start: 0.9510 (mp) cc_final: 0.9277 (mm) REVERT: D 480 LYS cc_start: 0.9168 (mmmm) cc_final: 0.8935 (mmmm) REVERT: D 486 LYS cc_start: 0.9292 (mttm) cc_final: 0.8805 (mttp) REVERT: D 492 ASP cc_start: 0.9229 (m-30) cc_final: 0.8967 (m-30) REVERT: E 443 LYS cc_start: 0.9492 (ptpt) cc_final: 0.9173 (ptpp) REVERT: E 461 ASP cc_start: 0.8887 (m-30) cc_final: 0.7561 (t70) REVERT: E 474 TYR cc_start: 0.9358 (t80) cc_final: 0.8918 (t80) REVERT: E 476 LEU cc_start: 0.9195 (mt) cc_final: 0.8988 (mt) REVERT: E 495 ASP cc_start: 0.9208 (m-30) cc_final: 0.8976 (m-30) REVERT: E 501 PHE cc_start: 0.8882 (t80) cc_final: 0.8216 (t80) REVERT: E 503 LYS cc_start: 0.9396 (pttm) cc_final: 0.9141 (pttm) REVERT: F 441 GLN cc_start: 0.8579 (tp-100) cc_final: 0.8176 (tp40) REVERT: F 446 ASP cc_start: 0.9079 (t70) cc_final: 0.8751 (t0) REVERT: F 459 SER cc_start: 0.9644 (m) cc_final: 0.9247 (p) REVERT: F 461 ASP cc_start: 0.9269 (t70) cc_final: 0.8544 (t70) REVERT: F 482 THR cc_start: 0.8479 (t) cc_final: 0.8039 (p) REVERT: F 515 MET cc_start: 0.6960 (tpt) cc_final: 0.6748 (tpp) REVERT: G 475 GLU cc_start: 0.8140 (mp0) cc_final: 0.7347 (tm-30) REVERT: G 500 GLU cc_start: 0.8032 (pm20) cc_final: 0.7795 (pm20) REVERT: G 515 MET cc_start: 0.3180 (mmp) cc_final: 0.2856 (mmp) REVERT: H 470 MET cc_start: 0.8842 (mpp) cc_final: 0.6773 (mpp) REVERT: H 472 GLU cc_start: 0.8854 (tt0) cc_final: 0.8457 (tt0) REVERT: H 473 ASP cc_start: 0.9135 (m-30) cc_final: 0.8770 (m-30) REVERT: H 478 SER cc_start: 0.9379 (m) cc_final: 0.9151 (p) REVERT: H 480 LYS cc_start: 0.8403 (ptpp) cc_final: 0.7460 (ptpp) REVERT: H 500 GLU cc_start: 0.8470 (mp0) cc_final: 0.8009 (pm20) REVERT: H 501 PHE cc_start: 0.8903 (t80) cc_final: 0.8081 (t80) REVERT: I 449 ASN cc_start: 0.9219 (m-40) cc_final: 0.8993 (m110) REVERT: I 458 GLN cc_start: 0.9040 (mt0) cc_final: 0.8715 (pt0) REVERT: I 470 MET cc_start: 0.8072 (mtt) cc_final: 0.7844 (mtt) REVERT: I 489 GLN cc_start: 0.8500 (pp30) cc_final: 0.8110 (pp30) REVERT: I 515 MET cc_start: 0.6573 (tpt) cc_final: 0.5468 (tpp) REVERT: J 445 GLU cc_start: 0.8847 (mp0) cc_final: 0.8460 (mp0) REVERT: J 449 ASN cc_start: 0.9268 (m-40) cc_final: 0.8908 (m-40) REVERT: J 451 MET cc_start: 0.9333 (tpp) cc_final: 0.9087 (tpp) REVERT: J 453 GLU cc_start: 0.9396 (tp30) cc_final: 0.8772 (tp30) REVERT: J 466 ARG cc_start: 0.8829 (mmm-85) cc_final: 0.8618 (mmm-85) REVERT: J 470 MET cc_start: 0.8838 (mtm) cc_final: 0.8475 (mtt) REVERT: J 489 GLN cc_start: 0.9156 (tm-30) cc_final: 0.8746 (tm-30) REVERT: J 494 THR cc_start: 0.9634 (m) cc_final: 0.9374 (m) REVERT: K 444 ARG cc_start: 0.7295 (ttm170) cc_final: 0.6764 (ptt-90) REVERT: K 449 ASN cc_start: 0.9414 (m110) cc_final: 0.9107 (m-40) REVERT: K 452 THR cc_start: 0.9281 (p) cc_final: 0.8908 (p) REVERT: K 456 LEU cc_start: 0.9729 (tp) cc_final: 0.9494 (tp) REVERT: K 470 MET cc_start: 0.7251 (mtm) cc_final: 0.6832 (mtt) REVERT: K 471 LYS cc_start: 0.9231 (mmmm) cc_final: 0.8836 (mtpp) REVERT: K 478 SER cc_start: 0.9595 (t) cc_final: 0.9372 (p) REVERT: K 486 LYS cc_start: 0.9288 (mtpt) cc_final: 0.9052 (mtpp) REVERT: L 437 GLN cc_start: 0.9412 (pt0) cc_final: 0.8696 (pm20) REVERT: L 440 ILE cc_start: 0.9748 (mm) cc_final: 0.9468 (mm) REVERT: L 441 GLN cc_start: 0.9291 (mt0) cc_final: 0.8991 (mm-40) REVERT: L 460 LEU cc_start: 0.9496 (mp) cc_final: 0.9231 (mp) REVERT: L 472 GLU cc_start: 0.8895 (pm20) cc_final: 0.8201 (pm20) REVERT: L 476 LEU cc_start: 0.9579 (mt) cc_final: 0.9180 (mt) REVERT: L 492 ASP cc_start: 0.9310 (m-30) cc_final: 0.8889 (m-30) outliers start: 0 outliers final: 0 residues processed: 464 average time/residue: 0.0980 time to fit residues: 60.9753 Evaluate side-chains 398 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 398 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 77 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 25 optimal weight: 20.0000 chunk 31 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 80 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 458 GLN ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 ASN B 449 ASN C 458 GLN D 458 GLN ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 512 ASN ** I 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN L 512 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.064625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.051225 restraints weight = 36675.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.053116 restraints weight = 24163.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.054555 restraints weight = 17770.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.055594 restraints weight = 13912.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.056378 restraints weight = 11533.633| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 2.0472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8328 Z= 0.166 Angle : 0.827 10.175 11184 Z= 0.437 Chirality : 0.047 0.198 1332 Planarity : 0.005 0.076 1440 Dihedral : 5.641 27.450 1092 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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 are not related in a simple way. whole: -0.52 (0.26), residues: 1020 helix: -0.05 (0.17), residues: 852 sheet: None (None), residues: 0 loop : -1.15 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 466 TYR 0.013 0.002 TYR I 474 PHE 0.013 0.002 PHE C 501 TRP 0.036 0.003 TRP I 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 8328) covalent geometry : angle 0.82731 / 0.44 (11184) hydrogen bonds : bond 0.03856 / 2.50 ( 529) hydrogen bonds : angle 4.83222 / 3.60 ( 1587) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 469 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 ASP cc_start: 0.8995 (m-30) cc_final: 0.8624 (t70) REVERT: A 480 LYS cc_start: 0.9546 (mmtt) cc_final: 0.9218 (mmmm) REVERT: A 488 ARG cc_start: 0.8374 (ttm-80) cc_final: 0.7925 (ttm-80) REVERT: A 492 ASP cc_start: 0.9093 (m-30) cc_final: 0.8579 (m-30) REVERT: A 501 PHE cc_start: 0.9279 (t80) cc_final: 0.8751 (t80) REVERT: A 513 LYS cc_start: 0.9052 (mmpt) cc_final: 0.8830 (mmmt) REVERT: B 453 GLU cc_start: 0.9338 (tp30) cc_final: 0.8785 (tp30) REVERT: B 467 ASP cc_start: 0.9229 (t0) cc_final: 0.9021 (t0) REVERT: C 438 GLN cc_start: 0.8961 (tt0) cc_final: 0.8508 (tp40) REVERT: C 440 ILE cc_start: 0.8978 (mt) cc_final: 0.8381 (mt) REVERT: C 441 GLN cc_start: 0.7958 (tp-100) cc_final: 0.6891 (tp-100) REVERT: C 444 ARG cc_start: 0.8590 (tpp-160) cc_final: 0.7911 (ttt-90) REVERT: C 446 ASP cc_start: 0.8430 (t0) cc_final: 0.8190 (t0) REVERT: C 450 GLN cc_start: 0.7512 (mt0) cc_final: 0.6604 (tm-30) REVERT: C 456 LEU cc_start: 0.9604 (tp) cc_final: 0.9222 (tp) REVERT: C 459 SER cc_start: 0.9793 (m) cc_final: 0.9576 (p) REVERT: C 461 ASP cc_start: 0.9094 (m-30) cc_final: 0.8579 (m-30) REVERT: C 471 LYS cc_start: 0.8921 (tmtt) cc_final: 0.8640 (tmtt) REVERT: C 480 LYS cc_start: 0.9420 (mmtm) cc_final: 0.9187 (mmtp) REVERT: C 486 LYS cc_start: 0.9414 (mttt) cc_final: 0.9111 (mttp) REVERT: C 491 LEU cc_start: 0.9260 (mt) cc_final: 0.8864 (mm) REVERT: D 441 GLN cc_start: 0.8306 (tp-100) cc_final: 0.8080 (tp-100) REVERT: D 449 ASN cc_start: 0.8845 (m110) cc_final: 0.8612 (m110) REVERT: D 458 GLN cc_start: 0.8957 (pt0) cc_final: 0.8719 (pt0) REVERT: D 497 GLN cc_start: 0.8209 (mm110) cc_final: 0.7742 (mm110) REVERT: E 443 LYS cc_start: 0.9522 (ptpt) cc_final: 0.8707 (ptpp) REVERT: E 446 ASP cc_start: 0.9152 (m-30) cc_final: 0.8716 (p0) REVERT: E 461 ASP cc_start: 0.8778 (m-30) cc_final: 0.7550 (t70) REVERT: E 474 TYR cc_start: 0.9336 (t80) cc_final: 0.9036 (t80) REVERT: E 486 LYS cc_start: 0.9216 (mttm) cc_final: 0.8855 (mmmm) REVERT: E 495 ASP cc_start: 0.9195 (m-30) cc_final: 0.8971 (m-30) REVERT: E 501 PHE cc_start: 0.8933 (t80) cc_final: 0.8262 (t80) REVERT: E 503 LYS cc_start: 0.9361 (pttm) cc_final: 0.9076 (pttm) REVERT: F 441 GLN cc_start: 0.8560 (tp-100) cc_final: 0.8170 (tp40) REVERT: F 446 ASP cc_start: 0.9088 (t70) cc_final: 0.8884 (t0) REVERT: F 459 SER cc_start: 0.9614 (m) cc_final: 0.9325 (p) REVERT: F 461 ASP cc_start: 0.9234 (t70) cc_final: 0.8527 (t70) REVERT: G 445 GLU cc_start: 0.8335 (pm20) cc_final: 0.7976 (pm20) REVERT: G 475 GLU cc_start: 0.8074 (mp0) cc_final: 0.7185 (tm-30) REVERT: G 500 GLU cc_start: 0.7942 (pm20) cc_final: 0.7715 (pm20) REVERT: G 507 GLN cc_start: 0.9299 (tp40) cc_final: 0.8932 (tm-30) REVERT: G 515 MET cc_start: 0.2163 (mmp) cc_final: 0.1637 (mmp) REVERT: H 453 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8447 (tm-30) REVERT: H 472 GLU cc_start: 0.8730 (tt0) cc_final: 0.8277 (tt0) REVERT: H 476 LEU cc_start: 0.9213 (mt) cc_final: 0.8987 (mt) REVERT: H 489 GLN cc_start: 0.7626 (pm20) cc_final: 0.7278 (pm20) REVERT: H 494 THR cc_start: 0.9502 (m) cc_final: 0.9210 (m) REVERT: H 500 GLU cc_start: 0.8538 (mp0) cc_final: 0.8109 (pm20) REVERT: H 501 PHE cc_start: 0.8871 (t80) cc_final: 0.8070 (t80) REVERT: I 449 ASN cc_start: 0.9188 (m-40) cc_final: 0.8975 (m110) REVERT: I 463 LEU cc_start: 0.9468 (mt) cc_final: 0.9247 (mt) REVERT: I 488 ARG cc_start: 0.8662 (ptp-110) cc_final: 0.8200 (ptp90) REVERT: I 515 MET cc_start: 0.6450 (tpt) cc_final: 0.5381 (tpp) REVERT: J 441 GLN cc_start: 0.8067 (tm-30) cc_final: 0.7828 (tm-30) REVERT: J 445 GLU cc_start: 0.8790 (mp0) cc_final: 0.8508 (mp0) REVERT: J 449 ASN cc_start: 0.9261 (m-40) cc_final: 0.8816 (m-40) REVERT: J 451 MET cc_start: 0.9303 (tpp) cc_final: 0.8934 (tpp) REVERT: J 453 GLU cc_start: 0.9452 (tp30) cc_final: 0.8869 (tp30) REVERT: J 489 GLN cc_start: 0.9114 (tm-30) cc_final: 0.8686 (tm-30) REVERT: J 495 ASP cc_start: 0.9484 (m-30) cc_final: 0.9272 (m-30) REVERT: K 444 ARG cc_start: 0.6869 (ttm170) cc_final: 0.6613 (ptt180) REVERT: K 452 THR cc_start: 0.9114 (p) cc_final: 0.8707 (p) REVERT: K 456 LEU cc_start: 0.9731 (tp) cc_final: 0.9496 (tp) REVERT: K 470 MET cc_start: 0.7064 (mtm) cc_final: 0.6669 (mtt) REVERT: K 471 LYS cc_start: 0.9211 (mmmm) cc_final: 0.8808 (mtpp) REVERT: K 478 SER cc_start: 0.9533 (t) cc_final: 0.9288 (p) REVERT: K 486 LYS cc_start: 0.9388 (mtpt) cc_final: 0.9177 (mttm) REVERT: K 489 GLN cc_start: 0.8906 (tm-30) cc_final: 0.8598 (tm-30) REVERT: K 499 GLU cc_start: 0.8747 (pp20) cc_final: 0.8032 (tp30) REVERT: K 509 LEU cc_start: 0.9425 (mm) cc_final: 0.9200 (mm) REVERT: L 437 GLN cc_start: 0.9336 (pt0) cc_final: 0.9111 (pm20) REVERT: L 460 LEU cc_start: 0.9520 (mp) cc_final: 0.9223 (mp) REVERT: L 472 GLU cc_start: 0.8863 (pm20) cc_final: 0.8552 (pm20) REVERT: L 492 ASP cc_start: 0.9305 (m-30) cc_final: 0.8794 (m-30) REVERT: L 501 PHE cc_start: 0.9201 (t80) cc_final: 0.8705 (t80) outliers start: 0 outliers final: 0 residues processed: 469 average time/residue: 0.0947 time to fit residues: 60.0447 Evaluate side-chains 400 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 50 optimal weight: 0.7980 chunk 91 optimal weight: 0.0980 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 78 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 450 GLN A 458 GLN ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 ASN C 458 GLN D 449 ASN D 458 GLN ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 438 GLN ** H 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 512 ASN ** I 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 437 GLN ** K 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN L 512 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.064502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.050791 restraints weight = 37005.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.052696 restraints weight = 24804.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.054085 restraints weight = 18385.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.055150 restraints weight = 14558.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.055994 restraints weight = 12113.532| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 2.0715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8328 Z= 0.167 Angle : 0.830 11.665 11184 Z= 0.438 Chirality : 0.047 0.190 1332 Planarity : 0.005 0.080 1440 Dihedral : 5.654 27.106 1092 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 20.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.11 % Allowed : 1.27 % Favored : 98.63 % 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 are not related in a simple way. whole: -0.56 (0.26), residues: 1020 helix: -0.09 (0.17), residues: 852 sheet: None (None), residues: 0 loop : -1.13 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 466 TYR 0.013 0.002 TYR K 474 PHE 0.030 0.003 PHE G 501 TRP 0.036 0.003 TRP I 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 8328) covalent geometry : angle 0.83011 / 0.44 (11184) hydrogen bonds : bond 0.03682 / 2.40 ( 529) hydrogen bonds : angle 4.80021 / 3.59 ( 1587) =============================================================================== Job complete usr+sys time: 1689.00 seconds wall clock time: 30 minutes 10.76 seconds (1810.76 seconds total)