Starting phenix.real_space_refine on Mon Nov 17 19:23:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5yrn_6842/11_2025/5yrn_6842.cif Found real_map, /net/cci-nas-00/data/ceres_data/5yrn_6842/11_2025/5yrn_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_6842/11_2025/5yrn_6842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5yrn_6842/11_2025/5yrn_6842.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5yrn_6842/11_2025/5yrn_6842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5yrn_6842/11_2025/5yrn_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-2.0-5881/lib/python3.9/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: 0.89, per 1000 atoms: 0.11 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: 0.66 Conformation dependent library (CDL) restraints added in 398.1 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: 0.26 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: 0.90 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.530 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5657 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 covalent geometry : bond 0.00702 ( 8328) covalent geometry : angle 1.00099 (11184) hydrogen bonds : bond 0.30098 ( 529) hydrogen bonds : angle 8.51466 ( 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 : 0.338 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: 0.1417 time to fit residues: 73.0392 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 : 0.316 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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: 0.6285 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 covalent geometry : bond 0.00357 ( 8328) covalent geometry : angle 0.71590 (11184) hydrogen bonds : bond 0.04689 ( 529) hydrogen bonds : angle 4.46178 ( 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 : 0.332 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: 0.8841 (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: 0.9023 (m) cc_final: 0.8715 (m) REVERT: B 460 LEU cc_start: 0.7493 (mt) cc_final: 0.7265 (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: 0.8756 (tptt) REVERT: C 480 LYS cc_start: 0.8590 (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: 0.8304 (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: 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: 0.7948 (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: 0.8023 (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: 0.1199 time to fit residues: 49.8614 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: 9.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3614 r_free = 0.3614 target = 0.083092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.067628 restraints weight = 35013.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.069825 restraints weight = 24804.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.071539 restraints weight = 18860.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.072885 restraints weight = 15023.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.073904 restraints weight = 12381.089| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 1.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8328 Z= 0.201 Angle : 0.762 6.302 11184 Z= 0.413 Chirality : 0.044 0.219 1332 Planarity : 0.005 0.060 1440 Dihedral : 5.634 26.579 1092 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.32 % Allowed : 5.80 % Favored : 93.88 % 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: -1.64 (0.23), residues: 1020 helix: -0.78 (0.15), residues: 924 sheet: None (None), residues: 0 loop : -2.31 (0.43), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 488 TYR 0.014 0.002 TYR L 474 PHE 0.013 0.003 PHE A 501 TRP 0.018 0.002 TRP H 439 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 8328) covalent geometry : angle 0.76179 (11184) hydrogen bonds : bond 0.04661 ( 529) hydrogen bonds : angle 4.60307 ( 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 402 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 399 time to evaluate : 0.339 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: A 443 LYS cc_start: 0.8096 (ptmm) cc_final: 0.7686 (ptmt) REVERT: A 461 ASP cc_start: 0.9043 (m-30) cc_final: 0.8687 (m-30) REVERT: A 471 LYS cc_start: 0.9241 (ptpp) cc_final: 0.8718 (ptmm) REVERT: A 480 LYS cc_start: 0.9488 (mmtt) cc_final: 0.9098 (mmmt) REVERT: A 486 LYS cc_start: 0.9387 (mtpt) cc_final: 0.9118 (mtmm) REVERT: A 488 ARG cc_start: 0.7930 (mtt-85) cc_final: 0.7668 (mtt90) REVERT: A 489 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8277 (tm-30) REVERT: A 511 ASP cc_start: 0.9063 (p0) cc_final: 0.8838 (p0) REVERT: B 458 GLN cc_start: 0.9012 (mp10) cc_final: 0.8798 (mp10) REVERT: B 470 MET cc_start: 0.8297 (mtm) cc_final: 0.7885 (mtt) REVERT: B 503 LYS cc_start: 0.9221 (ttmt) cc_final: 0.8921 (tptt) REVERT: C 440 ILE cc_start: 0.8187 (mt) cc_final: 0.7947 (mt) REVERT: C 441 GLN cc_start: 0.8298 (mm110) cc_final: 0.7997 (mm110) REVERT: C 447 ILE cc_start: 0.7461 (mt) cc_final: 0.7231 (mt) REVERT: C 461 ASP cc_start: 0.8751 (m-30) cc_final: 0.7450 (m-30) REVERT: D 450 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7666 (mt0) REVERT: D 470 MET cc_start: 0.8187 (ptp) cc_final: 0.7843 (ptt) REVERT: D 475 GLU cc_start: 0.9187 (tp30) cc_final: 0.8858 (tm-30) REVERT: D 483 ARG cc_start: 0.8002 (mtt180) cc_final: 0.6981 (ttp80) REVERT: D 507 GLN cc_start: 0.9124 (tm-30) cc_final: 0.8706 (tp-100) REVERT: D 513 LYS cc_start: 0.8670 (pptt) cc_final: 0.8402 (mmmt) REVERT: E 437 GLN cc_start: 0.9300 (tt0) cc_final: 0.8899 (tt0) REVERT: E 441 GLN cc_start: 0.9136 (mt0) cc_final: 0.8697 (mp10) REVERT: E 446 ASP cc_start: 0.9029 (m-30) cc_final: 0.8759 (m-30) REVERT: E 461 ASP cc_start: 0.8973 (m-30) cc_final: 0.8733 (m-30) REVERT: E 470 MET cc_start: 0.7594 (ptp) cc_final: 0.7013 (ptp) REVERT: E 473 ASP cc_start: 0.7795 (m-30) cc_final: 0.7009 (m-30) REVERT: E 480 LYS cc_start: 0.8979 (mtpt) cc_final: 0.8588 (ttmt) REVERT: E 483 ARG cc_start: 0.8118 (mtt180) cc_final: 0.7333 (ttm-80) REVERT: E 489 GLN cc_start: 0.8517 (mp10) cc_final: 0.8295 (mp10) REVERT: E 494 THR cc_start: 0.8811 (m) cc_final: 0.8582 (m) REVERT: E 497 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.7145 (mm-40) REVERT: F 460 LEU cc_start: 0.7420 (mt) cc_final: 0.7208 (mt) REVERT: F 515 MET cc_start: 0.7178 (tpt) cc_final: 0.6948 (tpt) REVERT: G 449 ASN cc_start: 0.8066 (t0) cc_final: 0.7741 (t0) REVERT: G 475 GLU cc_start: 0.7736 (mp0) cc_final: 0.6766 (pt0) REVERT: H 470 MET cc_start: 0.7759 (mpp) cc_final: 0.6903 (mpp) REVERT: H 477 VAL cc_start: 0.7491 (t) cc_final: 0.7246 (p) REVERT: H 486 LYS cc_start: 0.8319 (mtpt) cc_final: 0.7782 (ttmm) REVERT: I 476 LEU cc_start: 0.9242 (mt) cc_final: 0.8795 (mt) REVERT: I 477 VAL cc_start: 0.7234 (t) cc_final: 0.5687 (m) REVERT: I 482 THR cc_start: 0.8789 (p) cc_final: 0.8476 (p) REVERT: J 435 ILE cc_start: 0.7874 (mt) cc_final: 0.7665 (mt) REVERT: J 445 GLU cc_start: 0.7847 (mp0) cc_final: 0.7127 (mp0) REVERT: J 448 VAL cc_start: 0.8903 (t) cc_final: 0.8670 (m) REVERT: J 449 ASN cc_start: 0.9126 (m-40) cc_final: 0.8789 (m-40) REVERT: J 452 THR cc_start: 0.9183 (p) cc_final: 0.8483 (t) REVERT: J 467 ASP cc_start: 0.8310 (m-30) cc_final: 0.8054 (m-30) REVERT: J 470 MET cc_start: 0.7506 (mtm) cc_final: 0.7029 (mtm) REVERT: J 480 LYS cc_start: 0.8065 (pttm) cc_final: 0.7753 (pttm) REVERT: J 499 GLU cc_start: 0.8128 (pp20) cc_final: 0.7711 (tm-30) REVERT: J 503 LYS cc_start: 0.8703 (pptt) cc_final: 0.8433 (pttm) REVERT: K 444 ARG cc_start: 0.6243 (ttm170) cc_final: 0.5604 (pmt170) REVERT: K 480 LYS cc_start: 0.7268 (mmtt) cc_final: 0.6915 (mmtt) REVERT: L 441 GLN cc_start: 0.9176 (mt0) cc_final: 0.8431 (tm-30) REVERT: L 453 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8046 (tm-30) REVERT: L 486 LYS cc_start: 0.9083 (ttmm) cc_final: 0.8532 (ttmm) REVERT: L 495 ASP cc_start: 0.8938 (m-30) cc_final: 0.8666 (m-30) REVERT: L 500 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8811 (mm-30) outliers start: 3 outliers final: 0 residues processed: 400 average time/residue: 0.1117 time to fit residues: 57.5531 Evaluate side-chains 294 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 293 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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: 1.9990 chunk 18 optimal weight: 6.9990 chunk 8 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN A 512 ASN B 497 GLN C 449 ASN C 458 GLN D 458 GLN ** D 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.079051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.064146 restraints weight = 34429.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.066431 restraints weight = 23517.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.068163 restraints weight = 17417.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.069487 restraints weight = 13620.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.070536 restraints weight = 11129.018| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 1.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 8328 Z= 0.174 Angle : 0.690 9.421 11184 Z= 0.376 Chirality : 0.042 0.162 1332 Planarity : 0.005 0.067 1440 Dihedral : 5.307 21.506 1092 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.11 % Allowed : 3.69 % 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: -0.46 (0.25), residues: 1020 helix: -0.04 (0.16), residues: 888 sheet: None (None), residues: 0 loop : -1.12 (0.51), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 488 TYR 0.011 0.002 TYR G 474 PHE 0.027 0.003 PHE J 501 TRP 0.026 0.003 TRP K 439 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 8328) covalent geometry : angle 0.68963 (11184) hydrogen bonds : bond 0.03873 ( 529) hydrogen bonds : angle 4.40570 ( 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 424 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 423 time to evaluate : 0.343 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 430 THR cc_start: 0.6853 (m) cc_final: 0.6598 (t) REVERT: A 443 LYS cc_start: 0.8272 (ptmm) cc_final: 0.7992 (pmmt) REVERT: A 445 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8152 (mm-30) REVERT: A 461 ASP cc_start: 0.8909 (m-30) cc_final: 0.8522 (m-30) REVERT: A 468 LEU cc_start: 0.9231 (mp) cc_final: 0.8956 (mm) REVERT: A 471 LYS cc_start: 0.9143 (ptpp) cc_final: 0.8893 (ptmm) REVERT: A 476 LEU cc_start: 0.9521 (mt) cc_final: 0.9150 (mt) REVERT: A 480 LYS cc_start: 0.9545 (mmtt) cc_final: 0.9116 (mmmt) REVERT: A 486 LYS cc_start: 0.9563 (mtpt) cc_final: 0.9322 (mtmm) REVERT: A 489 GLN cc_start: 0.8384 (tm-30) cc_final: 0.8177 (tm-30) REVERT: A 492 ASP cc_start: 0.9266 (m-30) cc_final: 0.8906 (m-30) REVERT: A 513 LYS cc_start: 0.9019 (mmpt) cc_final: 0.8779 (mmmt) REVERT: B 458 GLN cc_start: 0.9061 (mp10) cc_final: 0.8811 (mt0) REVERT: B 460 LEU cc_start: 0.9100 (mt) cc_final: 0.8884 (mt) REVERT: B 470 MET cc_start: 0.8403 (mtm) cc_final: 0.7629 (mtt) REVERT: B 488 ARG cc_start: 0.8119 (mmt180) cc_final: 0.7502 (ptp-170) REVERT: B 515 MET cc_start: 0.7062 (tmm) cc_final: 0.6415 (tmm) REVERT: C 440 ILE cc_start: 0.8720 (mt) cc_final: 0.8392 (mt) REVERT: C 461 ASP cc_start: 0.8365 (m-30) cc_final: 0.7778 (m-30) REVERT: C 470 MET cc_start: 0.8647 (mtm) cc_final: 0.8246 (mtm) REVERT: C 478 SER cc_start: 0.9462 (t) cc_final: 0.9235 (p) REVERT: D 470 MET cc_start: 0.8457 (ptp) cc_final: 0.8115 (ptp) REVERT: D 475 GLU cc_start: 0.9239 (tp30) cc_final: 0.8899 (tm-30) REVERT: D 479 THR cc_start: 0.7862 (t) cc_final: 0.7563 (p) REVERT: D 483 ARG cc_start: 0.8318 (mtt180) cc_final: 0.7679 (ttp80) REVERT: D 493 THR cc_start: 0.8497 (m) cc_final: 0.8262 (p) REVERT: D 503 LYS cc_start: 0.8326 (pttm) cc_final: 0.8091 (pttm) REVERT: E 461 ASP cc_start: 0.8579 (m-30) cc_final: 0.7632 (t70) REVERT: E 470 MET cc_start: 0.7994 (ptp) cc_final: 0.7016 (ptp) REVERT: E 473 ASP cc_start: 0.8316 (m-30) cc_final: 0.7704 (m-30) REVERT: E 480 LYS cc_start: 0.9188 (mtpt) cc_final: 0.8859 (mtpp) REVERT: E 483 ARG cc_start: 0.8349 (mtt180) cc_final: 0.8126 (ttm170) REVERT: F 449 ASN cc_start: 0.8131 (m110) cc_final: 0.7842 (m-40) REVERT: F 458 GLN cc_start: 0.9291 (mm110) cc_final: 0.8258 (pt0) REVERT: F 461 ASP cc_start: 0.8752 (t70) cc_final: 0.7470 (t0) REVERT: G 475 GLU cc_start: 0.7830 (mp0) cc_final: 0.7162 (mm-30) REVERT: H 470 MET cc_start: 0.8449 (mpp) cc_final: 0.6147 (mpp) REVERT: H 473 ASP cc_start: 0.8954 (t0) cc_final: 0.8195 (m-30) REVERT: H 474 TYR cc_start: 0.8891 (t80) cc_final: 0.8641 (t80) REVERT: H 485 SER cc_start: 0.9082 (m) cc_final: 0.8515 (p) REVERT: H 493 THR cc_start: 0.9232 (p) cc_final: 0.8967 (p) REVERT: H 501 PHE cc_start: 0.8013 (t80) cc_final: 0.7705 (t80) REVERT: H 515 MET cc_start: 0.2740 (mmp) cc_final: 0.2095 (mmp) REVERT: I 447 ILE cc_start: 0.7963 (mt) cc_final: 0.7672 (mm) REVERT: I 482 THR cc_start: 0.8967 (p) cc_final: 0.7709 (p) REVERT: J 445 GLU cc_start: 0.8218 (mp0) cc_final: 0.7967 (mp0) REVERT: J 446 ASP cc_start: 0.8275 (t70) cc_final: 0.8058 (t0) REVERT: J 451 MET cc_start: 0.8801 (tpt) cc_final: 0.8491 (tpp) REVERT: J 452 THR cc_start: 0.8966 (p) cc_final: 0.8536 (t) REVERT: J 470 MET cc_start: 0.8036 (mtm) cc_final: 0.7788 (mtm) REVERT: J 500 GLU cc_start: 0.8892 (tp30) cc_final: 0.8592 (tp30) REVERT: K 444 ARG cc_start: 0.6494 (ttm170) cc_final: 0.6105 (ptt180) REVERT: K 449 ASN cc_start: 0.9094 (m110) cc_final: 0.8704 (m110) REVERT: K 453 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8273 (tm-30) REVERT: K 461 ASP cc_start: 0.8840 (t70) cc_final: 0.8451 (t70) REVERT: L 453 GLU cc_start: 0.8543 (tm-30) cc_final: 0.7760 (tm-30) REVERT: L 457 ASN cc_start: 0.8555 (p0) cc_final: 0.7829 (p0) REVERT: L 476 LEU cc_start: 0.9331 (mt) cc_final: 0.8994 (mt) REVERT: L 492 ASP cc_start: 0.9261 (m-30) cc_final: 0.8935 (m-30) REVERT: L 496 ILE cc_start: 0.8890 (pt) cc_final: 0.8560 (mp) REVERT: L 503 LYS cc_start: 0.9365 (mtpp) cc_final: 0.9129 (mtpp) outliers start: 1 outliers final: 1 residues processed: 424 average time/residue: 0.1119 time to fit residues: 61.5095 Evaluate side-chains 316 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 315 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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: 2.9990 chunk 56 optimal weight: 20.0000 chunk 9 optimal weight: 0.0980 chunk 72 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 ASN D 457 ASN D 497 GLN E 438 GLN F 450 GLN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 ASN H 514 GLN J 450 GLN J 497 GLN K 512 ASN L 450 GLN L 512 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.078153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.063080 restraints weight = 35128.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.065218 restraints weight = 24509.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.066878 restraints weight = 18577.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.068127 restraints weight = 14786.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.069004 restraints weight = 12243.328| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 1.4880 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= 0.156 Angle : 0.689 7.369 11184 Z= 0.371 Chirality : 0.043 0.177 1332 Planarity : 0.005 0.072 1440 Dihedral : 5.182 20.339 1092 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.42 % Allowed : 3.59 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.25), residues: 1020 helix: 0.22 (0.17), residues: 852 sheet: None (None), residues: 0 loop : -0.43 (0.47), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 483 TYR 0.019 0.002 TYR L 474 PHE 0.010 0.002 PHE C 501 TRP 0.020 0.003 TRP K 439 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8328) covalent geometry : angle 0.68925 (11184) hydrogen bonds : bond 0.03716 ( 529) hydrogen bonds : angle 4.18380 ( 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 422 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 418 time to evaluate : 0.348 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: 0.8781 (mt0) cc_final: 0.8151 (pp30) REVERT: A 468 LEU cc_start: 0.9348 (mp) cc_final: 0.9139 (mm) REVERT: A 471 LYS cc_start: 0.9228 (ptpp) cc_final: 0.8933 (ptmm) REVERT: A 476 LEU cc_start: 0.9688 (mt) cc_final: 0.8960 (mt) REVERT: A 480 LYS cc_start: 0.9530 (mmtt) cc_final: 0.8904 (mmmt) REVERT: A 486 LYS cc_start: 0.9541 (mtpt) cc_final: 0.9336 (mtmm) REVERT: A 492 ASP cc_start: 0.9314 (m-30) cc_final: 0.9012 (m-30) REVERT: A 513 LYS cc_start: 0.9090 (mmpt) cc_final: 0.8846 (mmmt) REVERT: B 476 LEU cc_start: 0.9321 (mt) cc_final: 0.9091 (mt) REVERT: B 488 ARG cc_start: 0.8070 (mmt180) cc_final: 0.7493 (ptp-170) REVERT: B 500 GLU cc_start: 0.7843 (pp20) cc_final: 0.7598 (pm20) REVERT: B 515 MET cc_start: 0.7051 (tmm) cc_final: 0.6618 (tmm) REVERT: C 440 ILE cc_start: 0.8814 (mt) cc_final: 0.8480 (mt) REVERT: C 441 GLN cc_start: 0.8530 (mm110) cc_final: 0.8253 (tp-100) REVERT: C 489 GLN cc_start: 0.7374 (mp10) cc_final: 0.7029 (mp10) REVERT: D 441 GLN cc_start: 0.8247 (tp-100) cc_final: 0.7868 (tp-100) REVERT: D 468 LEU cc_start: 0.9171 (mp) cc_final: 0.8790 (mt) REVERT: D 475 GLU cc_start: 0.9191 (tp30) cc_final: 0.8877 (pt0) REVERT: D 480 LYS cc_start: 0.8734 (mmmm) cc_final: 0.8398 (mmmm) REVERT: D 483 ARG cc_start: 0.8356 (mtt180) cc_final: 0.7688 (ttp80) REVERT: E 446 ASP cc_start: 0.9264 (m-30) cc_final: 0.9019 (m-30) REVERT: E 461 ASP cc_start: 0.8768 (m-30) cc_final: 0.7394 (t70) REVERT: E 470 MET cc_start: 0.8173 (ptp) cc_final: 0.7215 (ptp) REVERT: E 473 ASP cc_start: 0.8566 (m-30) cc_final: 0.8179 (m-30) REVERT: E 480 LYS cc_start: 0.9170 (mtpt) cc_final: 0.8852 (ttmt) REVERT: E 483 ARG cc_start: 0.8363 (mtt180) cc_final: 0.8021 (ttm170) REVERT: F 449 ASN cc_start: 0.8087 (m110) cc_final: 0.7810 (m-40) REVERT: F 450 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7963 (tp40) REVERT: G 446 ASP cc_start: 0.8783 (m-30) cc_final: 0.7808 (m-30) REVERT: G 461 ASP cc_start: 0.8591 (m-30) cc_final: 0.8315 (t0) REVERT: G 467 ASP cc_start: 0.8433 (t70) cc_final: 0.8224 (t70) REVERT: G 475 GLU cc_start: 0.8103 (mp0) cc_final: 0.7327 (tm-30) REVERT: G 485 SER cc_start: 0.8153 (m) cc_final: 0.7439 (m) REVERT: G 503 LYS cc_start: 0.9121 (ptpp) cc_final: 0.8733 (pttp) REVERT: G 506 VAL cc_start: 0.9317 (t) cc_final: 0.8628 (t) REVERT: G 507 GLN cc_start: 0.9200 (tp-100) cc_final: 0.8867 (mm-40) REVERT: H 470 MET cc_start: 0.8832 (mpp) cc_final: 0.7612 (mpp) REVERT: H 488 ARG cc_start: 0.7948 (mmt90) cc_final: 0.6075 (mmt90) REVERT: H 489 GLN cc_start: 0.8218 (tt0) cc_final: 0.7640 (tt0) REVERT: H 515 MET cc_start: 0.3080 (mmp) cc_final: 0.2425 (mmp) REVERT: I 447 ILE cc_start: 0.8036 (mt) cc_final: 0.7795 (mm) REVERT: I 461 ASP cc_start: 0.8376 (t70) cc_final: 0.8008 (t70) REVERT: I 475 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8283 (mt-10) REVERT: J 430 THR cc_start: 0.6474 (m) cc_final: 0.6246 (t) REVERT: J 441 GLN cc_start: 0.7610 (tm-30) cc_final: 0.7051 (tm-30) REVERT: J 445 GLU cc_start: 0.8368 (mp0) cc_final: 0.7864 (mp0) REVERT: J 449 ASN cc_start: 0.9290 (m-40) cc_final: 0.8968 (m-40) REVERT: J 470 MET cc_start: 0.8904 (mtm) cc_final: 0.8491 (mtt) REVERT: J 475 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8416 (mt-10) REVERT: J 476 LEU cc_start: 0.9321 (mt) cc_final: 0.9070 (mt) REVERT: J 501 PHE cc_start: 0.8988 (t80) cc_final: 0.8787 (t80) REVERT: K 444 ARG cc_start: 0.6715 (ttm170) cc_final: 0.6192 (ptt180) REVERT: K 449 ASN cc_start: 0.9080 (m110) cc_final: 0.8636 (m110) REVERT: K 456 LEU cc_start: 0.8776 (tp) cc_final: 0.8499 (tp) REVERT: K 461 ASP cc_start: 0.8883 (t70) cc_final: 0.8023 (m-30) REVERT: K 509 LEU cc_start: 0.8891 (mt) cc_final: 0.8662 (mt) REVERT: L 437 GLN cc_start: 0.9436 (pt0) cc_final: 0.9046 (pm20) REVERT: L 438 GLN cc_start: 0.9164 (tm-30) cc_final: 0.8804 (tm-30) REVERT: L 441 GLN cc_start: 0.9102 (mt0) cc_final: 0.8428 (pp30) REVERT: L 442 SER cc_start: 0.9217 (t) cc_final: 0.8272 (p) REVERT: L 472 GLU cc_start: 0.7577 (tt0) cc_final: 0.6937 (tt0) REVERT: L 489 GLN cc_start: 0.8804 (mt0) cc_final: 0.8369 (tt0) REVERT: L 492 ASP cc_start: 0.9355 (m-30) cc_final: 0.9018 (m-30) REVERT: L 496 ILE cc_start: 0.8858 (pt) cc_final: 0.8643 (mp) REVERT: L 503 LYS cc_start: 0.9336 (mtpp) cc_final: 0.9023 (mtpp) outliers start: 4 outliers final: 0 residues processed: 420 average time/residue: 0.1082 time to fit residues: 59.5142 Evaluate side-chains 333 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 332 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: 0.7980 chunk 21 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 92 optimal weight: 0.0170 chunk 19 optimal weight: 0.7980 chunk 13 optimal weight: 8.9990 chunk 46 optimal weight: 0.0010 chunk 16 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 overall best weight: 0.5226 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** D 441 GLN D 457 ASN E 437 GLN E 438 GLN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 438 GLN G 512 ASN ** I 437 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 = 0.3548 r_free = 0.3548 target = 0.076849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.061901 restraints weight = 35259.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.064086 restraints weight = 24160.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.065723 restraints weight = 17997.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.066995 restraints weight = 14231.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.067990 restraints weight = 11732.009| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 1.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8328 Z= 0.138 Angle : 0.683 6.597 11184 Z= 0.369 Chirality : 0.042 0.150 1332 Planarity : 0.004 0.074 1440 Dihedral : 5.040 19.621 1092 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.21 % Allowed : 2.00 % Favored : 97.78 % 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: -0.15 (0.25), residues: 1020 helix: 0.19 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -1.21 (0.53), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 483 TYR 0.019 0.002 TYR H 474 PHE 0.017 0.002 PHE H 501 TRP 0.029 0.003 TRP A 439 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8328) covalent geometry : angle 0.68252 (11184) hydrogen bonds : bond 0.03415 ( 529) hydrogen bonds : angle 4.31975 ( 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 418 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 416 time to evaluate : 0.276 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 450 GLN cc_start: 0.8888 (mt0) cc_final: 0.8588 (pt0) REVERT: A 458 GLN cc_start: 0.9417 (pt0) cc_final: 0.9212 (pt0) REVERT: A 461 ASP cc_start: 0.9036 (m-30) cc_final: 0.8338 (t70) REVERT: A 471 LYS cc_start: 0.9169 (ptpp) cc_final: 0.8931 (ptmm) REVERT: A 472 GLU cc_start: 0.9176 (mp0) cc_final: 0.8647 (pm20) REVERT: A 473 ASP cc_start: 0.9263 (m-30) cc_final: 0.8748 (m-30) REVERT: A 491 LEU cc_start: 0.9577 (mp) cc_final: 0.9345 (mt) REVERT: A 492 ASP cc_start: 0.9053 (m-30) cc_final: 0.8664 (m-30) REVERT: A 494 THR cc_start: 0.9629 (m) cc_final: 0.9409 (p) REVERT: A 495 ASP cc_start: 0.9098 (p0) cc_final: 0.8692 (p0) REVERT: A 513 LYS cc_start: 0.9050 (mmpt) cc_final: 0.8797 (mmmt) REVERT: B 448 VAL cc_start: 0.6297 (t) cc_final: 0.5990 (t) REVERT: B 449 ASN cc_start: 0.7359 (t0) cc_final: 0.7136 (t0) REVERT: B 469 ILE cc_start: 0.9338 (tt) cc_final: 0.9107 (tt) REVERT: B 476 LEU cc_start: 0.9339 (mt) cc_final: 0.9059 (mt) REVERT: B 500 GLU cc_start: 0.7916 (pp20) cc_final: 0.7200 (pm20) REVERT: B 515 MET cc_start: 0.7028 (tmm) cc_final: 0.6580 (tmm) REVERT: C 441 GLN cc_start: 0.8476 (mm110) cc_final: 0.8146 (tp-100) REVERT: C 456 LEU cc_start: 0.9356 (tp) cc_final: 0.9155 (tp) REVERT: C 461 ASP cc_start: 0.8981 (m-30) cc_final: 0.7618 (m-30) REVERT: C 470 MET cc_start: 0.8667 (mtp) cc_final: 0.8291 (mtm) REVERT: D 474 TYR cc_start: 0.9148 (t80) cc_final: 0.8925 (t80) REVERT: D 483 ARG cc_start: 0.8332 (mtt180) cc_final: 0.7923 (ttp80) REVERT: E 443 LYS cc_start: 0.9338 (ptpt) cc_final: 0.8789 (ptpp) REVERT: E 445 GLU cc_start: 0.8900 (pm20) cc_final: 0.8547 (pm20) REVERT: E 446 ASP cc_start: 0.9244 (m-30) cc_final: 0.8756 (m-30) REVERT: E 453 GLU cc_start: 0.8847 (tp30) cc_final: 0.8018 (tp30) REVERT: E 461 ASP cc_start: 0.8543 (m-30) cc_final: 0.7082 (t70) REVERT: E 480 LYS cc_start: 0.9238 (mtpt) cc_final: 0.8962 (ttmt) REVERT: F 449 ASN cc_start: 0.8261 (m110) cc_final: 0.7986 (m-40) REVERT: F 460 LEU cc_start: 0.8436 (pp) cc_final: 0.8222 (pp) REVERT: F 467 ASP cc_start: 0.8049 (t70) cc_final: 0.7584 (m-30) REVERT: G 446 ASP cc_start: 0.8798 (m-30) cc_final: 0.7708 (m-30) REVERT: G 467 ASP cc_start: 0.8458 (t70) cc_final: 0.8130 (t70) REVERT: G 475 GLU cc_start: 0.7806 (mp0) cc_final: 0.7240 (tp30) REVERT: G 485 SER cc_start: 0.8209 (m) cc_final: 0.7991 (p) REVERT: H 441 GLN cc_start: 0.8688 (pp30) cc_final: 0.8302 (pp30) REVERT: H 470 MET cc_start: 0.8839 (mpp) cc_final: 0.7838 (mpp) REVERT: H 480 LYS cc_start: 0.7945 (ptpp) cc_final: 0.7550 (ptpp) REVERT: H 488 ARG cc_start: 0.7799 (mmt180) cc_final: 0.7251 (mmt90) REVERT: H 489 GLN cc_start: 0.8259 (tt0) cc_final: 0.7895 (tt0) REVERT: H 515 MET cc_start: 0.3103 (mmp) cc_final: 0.2530 (mmp) REVERT: I 461 ASP cc_start: 0.8574 (t70) cc_final: 0.7774 (t70) REVERT: I 475 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8480 (mt-10) REVERT: I 476 LEU cc_start: 0.9400 (mt) cc_final: 0.9149 (mt) REVERT: I 479 THR cc_start: 0.8978 (m) cc_final: 0.8603 (p) REVERT: I 482 THR cc_start: 0.8673 (t) cc_final: 0.7618 (t) REVERT: I 484 THR cc_start: 0.8337 (p) cc_final: 0.7998 (p) REVERT: J 430 THR cc_start: 0.6762 (m) cc_final: 0.6529 (t) REVERT: J 441 GLN cc_start: 0.7696 (tm-30) cc_final: 0.7186 (tm-30) REVERT: J 445 GLU cc_start: 0.8549 (mp0) cc_final: 0.8134 (mp0) REVERT: J 449 ASN cc_start: 0.9249 (m-40) cc_final: 0.8919 (m-40) REVERT: J 457 ASN cc_start: 0.8994 (p0) cc_final: 0.8459 (p0) REVERT: J 470 MET cc_start: 0.8697 (mtm) cc_final: 0.8476 (mtt) REVERT: J 472 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8458 (mt-10) REVERT: J 475 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8302 (mt-10) REVERT: J 480 LYS cc_start: 0.8331 (ptpp) cc_final: 0.8059 (ptpp) REVERT: K 444 ARG cc_start: 0.6469 (ttm170) cc_final: 0.5982 (ptt-90) REVERT: K 449 ASN cc_start: 0.8962 (m110) cc_final: 0.8484 (m110) REVERT: K 456 LEU cc_start: 0.8822 (tp) cc_final: 0.8377 (tp) REVERT: K 461 ASP cc_start: 0.8853 (t70) cc_final: 0.8495 (m-30) REVERT: K 486 LYS cc_start: 0.8472 (mtpt) cc_final: 0.8195 (mttm) REVERT: K 509 LEU cc_start: 0.8901 (mt) cc_final: 0.8606 (mt) REVERT: L 441 GLN cc_start: 0.8959 (mt0) cc_final: 0.8529 (tm-30) REVERT: L 472 GLU cc_start: 0.7216 (tt0) cc_final: 0.6797 (tt0) REVERT: L 476 LEU cc_start: 0.9294 (mt) cc_final: 0.9077 (mt) REVERT: L 489 GLN cc_start: 0.8768 (mt0) cc_final: 0.8509 (mt0) REVERT: L 492 ASP cc_start: 0.9373 (m-30) cc_final: 0.8896 (m-30) REVERT: L 496 ILE cc_start: 0.8812 (pt) cc_final: 0.8598 (mp) REVERT: L 503 LYS cc_start: 0.9356 (mtpp) cc_final: 0.9123 (mtpp) REVERT: L 504 VAL cc_start: 0.9390 (t) cc_final: 0.9189 (m) outliers start: 2 outliers final: 1 residues processed: 417 average time/residue: 0.1070 time to fit residues: 58.4734 Evaluate side-chains 339 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 338 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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: 0.9990 chunk 46 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 48 optimal weight: 20.0000 chunk 6 optimal weight: 0.1980 chunk 82 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 57 optimal weight: 0.0670 overall best weight: 0.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** B 489 GLN D 457 ASN F 458 GLN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 437 GLN I 437 GLN K 512 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 = 0.3572 r_free = 0.3572 target = 0.079235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.064458 restraints weight = 35457.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.066687 restraints weight = 24040.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.068366 restraints weight = 17810.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.069643 restraints weight = 13972.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.070628 restraints weight = 11396.347| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 1.5863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8328 Z= 0.140 Angle : 0.695 7.643 11184 Z= 0.372 Chirality : 0.043 0.180 1332 Planarity : 0.004 0.073 1440 Dihedral : 5.170 28.920 1092 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % 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: 0.22 (0.25), residues: 1020 helix: 0.41 (0.17), residues: 852 sheet: None (None), residues: 0 loop : -0.63 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 483 TYR 0.015 0.001 TYR H 474 PHE 0.009 0.002 PHE E 501 TRP 0.034 0.003 TRP A 439 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8328) covalent geometry : angle 0.69513 (11184) hydrogen bonds : bond 0.03323 ( 529) hydrogen bonds : angle 4.28901 ( 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 413 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7835 (mm-30) REVERT: A 450 GLN cc_start: 0.8781 (mt0) cc_final: 0.8102 (pp30) REVERT: A 461 ASP cc_start: 0.9036 (m-30) cc_final: 0.8324 (t70) REVERT: A 471 LYS cc_start: 0.9134 (ptpp) cc_final: 0.8672 (ptmm) REVERT: A 492 ASP cc_start: 0.9040 (m-30) cc_final: 0.8498 (m-30) REVERT: A 513 LYS cc_start: 0.9010 (mmpt) cc_final: 0.8783 (mmmt) REVERT: B 448 VAL cc_start: 0.6811 (t) cc_final: 0.6525 (t) REVERT: B 449 ASN cc_start: 0.7520 (t0) cc_final: 0.7306 (t0) REVERT: B 475 GLU cc_start: 0.8714 (pt0) cc_final: 0.8040 (pt0) REVERT: B 500 GLU cc_start: 0.7872 (pp20) cc_final: 0.7600 (pm20) REVERT: C 441 GLN cc_start: 0.8376 (mm110) cc_final: 0.8017 (tp-100) REVERT: C 461 ASP cc_start: 0.8601 (m-30) cc_final: 0.7909 (m-30) REVERT: C 470 MET cc_start: 0.8625 (mtp) cc_final: 0.8319 (mtm) REVERT: C 491 LEU cc_start: 0.8475 (mp) cc_final: 0.8134 (tt) REVERT: D 458 GLN cc_start: 0.9001 (mp10) cc_final: 0.8546 (pt0) REVERT: D 474 TYR cc_start: 0.9120 (t80) cc_final: 0.8849 (t80) REVERT: D 476 LEU cc_start: 0.8905 (mt) cc_final: 0.8589 (mt) REVERT: D 480 LYS cc_start: 0.9074 (ttmm) cc_final: 0.8717 (ttmm) REVERT: E 445 GLU cc_start: 0.8863 (pm20) cc_final: 0.8538 (pm20) REVERT: E 446 ASP cc_start: 0.9151 (m-30) cc_final: 0.8696 (m-30) REVERT: E 461 ASP cc_start: 0.8023 (m-30) cc_final: 0.7036 (t70) REVERT: E 466 ARG cc_start: 0.8606 (ptp90) cc_final: 0.8374 (ptp90) REVERT: E 471 LYS cc_start: 0.8711 (mttt) cc_final: 0.8361 (pttt) REVERT: E 473 ASP cc_start: 0.8813 (m-30) cc_final: 0.8555 (m-30) REVERT: E 480 LYS cc_start: 0.9134 (mtpt) cc_final: 0.8877 (ttmt) REVERT: F 449 ASN cc_start: 0.8216 (m110) cc_final: 0.7941 (m-40) REVERT: F 460 LEU cc_start: 0.8556 (pp) cc_final: 0.8326 (pp) REVERT: F 467 ASP cc_start: 0.8136 (t70) cc_final: 0.7666 (m-30) REVERT: G 441 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7956 (tm-30) REVERT: G 446 ASP cc_start: 0.8340 (m-30) cc_final: 0.8027 (m-30) REVERT: G 467 ASP cc_start: 0.8532 (t70) cc_final: 0.8212 (t70) REVERT: G 475 GLU cc_start: 0.8092 (mp0) cc_final: 0.7126 (tm-30) REVERT: H 438 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8508 (tm-30) REVERT: H 441 GLN cc_start: 0.8556 (pp30) cc_final: 0.8143 (pp30) REVERT: H 470 MET cc_start: 0.8868 (mpp) cc_final: 0.7784 (mpp) REVERT: H 488 ARG cc_start: 0.7979 (mmt180) cc_final: 0.7135 (mmm-85) REVERT: H 489 GLN cc_start: 0.8371 (tt0) cc_final: 0.8167 (tt0) REVERT: H 507 GLN cc_start: 0.8898 (mp10) cc_final: 0.8642 (mp10) REVERT: H 515 MET cc_start: 0.3222 (mmp) cc_final: 0.2604 (mmp) REVERT: I 461 ASP cc_start: 0.8218 (t70) cc_final: 0.7555 (t70) REVERT: I 475 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8737 (mt-10) REVERT: I 476 LEU cc_start: 0.9429 (mt) cc_final: 0.9123 (mt) REVERT: I 479 THR cc_start: 0.9046 (m) cc_final: 0.8665 (p) REVERT: I 480 LYS cc_start: 0.8872 (mttp) cc_final: 0.8632 (mttp) REVERT: I 484 THR cc_start: 0.8498 (p) cc_final: 0.7953 (p) REVERT: J 445 GLU cc_start: 0.8550 (mp0) cc_final: 0.8258 (mp0) REVERT: J 449 ASN cc_start: 0.9198 (m-40) cc_final: 0.8858 (m-40) REVERT: J 468 LEU cc_start: 0.9307 (mm) cc_final: 0.9079 (mp) REVERT: J 470 MET cc_start: 0.8888 (mtm) cc_final: 0.8592 (mtm) REVERT: J 472 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8245 (mt-10) REVERT: J 474 TYR cc_start: 0.9247 (t80) cc_final: 0.8985 (t80) REVERT: J 475 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8580 (mt-10) REVERT: K 444 ARG cc_start: 0.6547 (ttm170) cc_final: 0.5895 (ptt180) REVERT: K 449 ASN cc_start: 0.8848 (m110) cc_final: 0.8289 (m110) REVERT: K 450 GLN cc_start: 0.8686 (mt0) cc_final: 0.8173 (tt0) REVERT: K 456 LEU cc_start: 0.8885 (tp) cc_final: 0.8518 (tp) REVERT: K 461 ASP cc_start: 0.8846 (t70) cc_final: 0.8465 (m-30) REVERT: K 464 LEU cc_start: 0.9137 (mp) cc_final: 0.8811 (mt) REVERT: K 468 LEU cc_start: 0.8711 (mt) cc_final: 0.8462 (mp) REVERT: K 486 LYS cc_start: 0.8652 (mtpt) cc_final: 0.7763 (mtpp) REVERT: K 507 GLN cc_start: 0.8899 (tm-30) cc_final: 0.8444 (tm-30) REVERT: L 446 ASP cc_start: 0.9103 (p0) cc_final: 0.8602 (p0) REVERT: L 450 GLN cc_start: 0.8928 (mp10) cc_final: 0.8669 (mp10) REVERT: L 476 LEU cc_start: 0.9279 (mt) cc_final: 0.9040 (mt) REVERT: L 492 ASP cc_start: 0.9417 (m-30) cc_final: 0.9093 (m-30) REVERT: L 500 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8686 (mm-30) REVERT: L 501 PHE cc_start: 0.8601 (t80) cc_final: 0.8134 (t80) REVERT: L 503 LYS cc_start: 0.9411 (mtpp) cc_final: 0.9112 (mtpp) outliers start: 0 outliers final: 0 residues processed: 413 average time/residue: 0.1010 time to fit residues: 55.4598 Evaluate side-chains 333 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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: 5.9990 chunk 47 optimal weight: 0.4980 chunk 72 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 457 ASN ** F 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** G 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 512 ASN ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN L 512 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.072227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.058856 restraints weight = 35838.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.060937 restraints weight = 23375.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.062554 restraints weight = 16953.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.063792 restraints weight = 12992.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.064719 restraints weight = 10440.854| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 1.7608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8328 Z= 0.186 Angle : 0.762 8.108 11184 Z= 0.412 Chirality : 0.045 0.177 1332 Planarity : 0.005 0.072 1440 Dihedral : 5.364 29.541 1092 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % 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: -0.68 (0.25), residues: 1020 helix: -0.06 (0.16), residues: 900 sheet: None (None), residues: 0 loop : -2.44 (0.46), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 488 TYR 0.021 0.002 TYR H 474 PHE 0.015 0.002 PHE H 501 TRP 0.033 0.004 TRP A 439 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 8328) covalent geometry : angle 0.76212 (11184) hydrogen bonds : bond 0.03560 ( 529) hydrogen bonds : angle 4.50556 ( 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 440 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 440 time to evaluate : 0.366 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 450 GLN cc_start: 0.8890 (mt0) cc_final: 0.8053 (pp30) REVERT: A 461 ASP cc_start: 0.9080 (m-30) cc_final: 0.8869 (t70) REVERT: A 471 LYS cc_start: 0.9207 (ptpp) cc_final: 0.8916 (ttpp) REVERT: A 488 ARG cc_start: 0.8247 (ttm-80) cc_final: 0.7809 (ttm-80) REVERT: A 492 ASP cc_start: 0.9213 (m-30) cc_final: 0.8784 (m-30) REVERT: A 500 GLU cc_start: 0.8411 (pm20) cc_final: 0.8054 (pm20) REVERT: A 513 LYS cc_start: 0.9056 (mmpt) cc_final: 0.8808 (mmmt) REVERT: B 443 LYS cc_start: 0.8063 (tptp) cc_final: 0.7729 (tppt) REVERT: B 448 VAL cc_start: 0.7667 (t) cc_final: 0.7415 (t) REVERT: B 450 GLN cc_start: 0.7165 (mt0) cc_final: 0.6928 (mt0) REVERT: B 458 GLN cc_start: 0.9119 (mp10) cc_final: 0.8889 (pm20) REVERT: B 492 ASP cc_start: 0.8649 (m-30) cc_final: 0.8402 (m-30) REVERT: B 503 LYS cc_start: 0.9223 (pttp) cc_final: 0.9004 (pttm) REVERT: C 441 GLN cc_start: 0.8324 (mm110) cc_final: 0.7791 (tp-100) REVERT: C 470 MET cc_start: 0.9047 (mtp) cc_final: 0.8828 (mtt) REVERT: C 491 LEU cc_start: 0.9054 (mp) cc_final: 0.8280 (mt) REVERT: C 492 ASP cc_start: 0.9334 (m-30) cc_final: 0.9097 (m-30) REVERT: D 441 GLN cc_start: 0.8692 (tp-100) cc_final: 0.8309 (tm-30) REVERT: D 466 ARG cc_start: 0.9000 (mpp80) cc_final: 0.8781 (mpp80) REVERT: D 474 TYR cc_start: 0.9453 (t80) cc_final: 0.9153 (t80) REVERT: D 478 SER cc_start: 0.9473 (t) cc_final: 0.9262 (p) REVERT: D 480 LYS cc_start: 0.9048 (ttmm) cc_final: 0.8629 (ttmm) REVERT: E 445 GLU cc_start: 0.8840 (pm20) cc_final: 0.8540 (pm20) REVERT: E 446 ASP cc_start: 0.9042 (m-30) cc_final: 0.8796 (m-30) REVERT: E 461 ASP cc_start: 0.8180 (m-30) cc_final: 0.7119 (t70) REVERT: E 471 LYS cc_start: 0.8652 (mttt) cc_final: 0.8419 (pttt) REVERT: E 473 ASP cc_start: 0.8999 (m-30) cc_final: 0.8757 (m-30) REVERT: E 480 LYS cc_start: 0.9192 (mtpt) cc_final: 0.8886 (ttmm) REVERT: E 489 GLN cc_start: 0.8705 (mp10) cc_final: 0.8217 (mp10) REVERT: E 503 LYS cc_start: 0.9366 (pttm) cc_final: 0.8993 (pttm) REVERT: F 449 ASN cc_start: 0.8560 (m110) cc_final: 0.8232 (p0) REVERT: F 470 MET cc_start: 0.6453 (ttt) cc_final: 0.6107 (mtm) REVERT: G 446 ASP cc_start: 0.8708 (m-30) cc_final: 0.7864 (m-30) REVERT: G 475 GLU cc_start: 0.8059 (mp0) cc_final: 0.7163 (tm-30) REVERT: G 480 LYS cc_start: 0.7881 (ttpt) cc_final: 0.7679 (ttpt) REVERT: G 488 ARG cc_start: 0.7985 (mtt90) cc_final: 0.7691 (mmt90) REVERT: G 503 LYS cc_start: 0.9340 (ptpp) cc_final: 0.9093 (pttp) REVERT: H 470 MET cc_start: 0.9088 (mpp) cc_final: 0.7845 (mpp) REVERT: H 476 LEU cc_start: 0.9309 (mt) cc_final: 0.8633 (mt) REVERT: H 480 LYS cc_start: 0.8371 (ptpp) cc_final: 0.7962 (ptpp) REVERT: H 488 ARG cc_start: 0.7882 (mmt180) cc_final: 0.7128 (mmt-90) REVERT: H 515 MET cc_start: 0.3700 (mmp) cc_final: 0.2997 (mmp) REVERT: I 445 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8160 (mm-30) REVERT: I 463 LEU cc_start: 0.9404 (mt) cc_final: 0.9171 (mt) REVERT: I 476 LEU cc_start: 0.9503 (mt) cc_final: 0.9167 (mt) REVERT: I 479 THR cc_start: 0.9271 (m) cc_final: 0.9069 (p) REVERT: I 480 LYS cc_start: 0.8794 (mttp) cc_final: 0.8467 (mttp) REVERT: I 484 THR cc_start: 0.8511 (p) cc_final: 0.7782 (p) REVERT: I 488 ARG cc_start: 0.8228 (mtm110) cc_final: 0.7806 (ptp-110) REVERT: J 441 GLN cc_start: 0.7427 (tm-30) cc_final: 0.7164 (tm-30) REVERT: J 453 GLU cc_start: 0.9269 (tp30) cc_final: 0.8953 (tp30) REVERT: J 469 ILE cc_start: 0.9132 (tp) cc_final: 0.8931 (tp) REVERT: J 470 MET cc_start: 0.9138 (mtm) cc_final: 0.8218 (mtt) REVERT: J 472 GLU cc_start: 0.8595 (mt-10) cc_final: 0.7676 (mt-10) REVERT: J 492 ASP cc_start: 0.9008 (m-30) cc_final: 0.8803 (m-30) REVERT: J 495 ASP cc_start: 0.9310 (m-30) cc_final: 0.9050 (m-30) REVERT: J 501 PHE cc_start: 0.9275 (t80) cc_final: 0.8737 (t80) REVERT: K 444 ARG cc_start: 0.6948 (ttm170) cc_final: 0.6072 (ptt-90) REVERT: K 449 ASN cc_start: 0.9237 (m110) cc_final: 0.8802 (m-40) REVERT: K 456 LEU cc_start: 0.9388 (tp) cc_final: 0.9119 (tp) REVERT: K 486 LYS cc_start: 0.9056 (mtpt) cc_final: 0.8672 (mttm) REVERT: L 441 GLN cc_start: 0.9089 (mt0) cc_final: 0.8734 (tm-30) REVERT: L 446 ASP cc_start: 0.9060 (p0) cc_final: 0.8700 (p0) REVERT: L 469 ILE cc_start: 0.8792 (tp) cc_final: 0.8516 (tp) REVERT: L 472 GLU cc_start: 0.8753 (pm20) cc_final: 0.8170 (pm20) REVERT: L 476 LEU cc_start: 0.9369 (mt) cc_final: 0.9056 (mt) REVERT: L 492 ASP cc_start: 0.9334 (m-30) cc_final: 0.9121 (m-30) REVERT: L 499 GLU cc_start: 0.8616 (pp20) cc_final: 0.8374 (pp20) REVERT: L 500 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8800 (mm-30) REVERT: L 503 LYS cc_start: 0.9419 (mtpp) cc_final: 0.9016 (mtpp) outliers start: 0 outliers final: 0 residues processed: 440 average time/residue: 0.1033 time to fit residues: 59.8546 Evaluate side-chains 354 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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: 9.9990 chunk 67 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 70 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 5 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN A 512 ASN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN B 489 GLN D 458 GLN F 441 GLN F 457 ASN F 458 GLN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 514 GLN H 512 ASN I 512 ASN ** J 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 437 GLN K 458 GLN ** K 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN L 512 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.070130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.056603 restraints weight = 36780.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.058621 restraints weight = 24258.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.060175 restraints weight = 17778.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.061333 restraints weight = 13866.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.062243 restraints weight = 11311.518| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 1.8510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8328 Z= 0.183 Angle : 0.801 8.210 11184 Z= 0.427 Chirality : 0.046 0.182 1332 Planarity : 0.005 0.078 1440 Dihedral : 5.484 29.167 1092 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.11 % Allowed : 1.48 % Favored : 98.42 % 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: -0.86 (0.25), residues: 1020 helix: -0.24 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -1.84 (0.50), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG H 488 TYR 0.021 0.002 TYR H 474 PHE 0.011 0.002 PHE E 501 TRP 0.036 0.003 TRP I 439 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 8328) covalent geometry : angle 0.80071 (11184) hydrogen bonds : bond 0.03543 ( 529) hydrogen bonds : angle 4.77577 ( 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 445 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 444 time to evaluate : 0.359 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 450 GLN cc_start: 0.9006 (mt0) cc_final: 0.8222 (pp30) REVERT: A 458 GLN cc_start: 0.9239 (pt0) cc_final: 0.8940 (pt0) REVERT: A 461 ASP cc_start: 0.9088 (m-30) cc_final: 0.8824 (t70) REVERT: A 471 LYS cc_start: 0.9181 (ptpp) cc_final: 0.8826 (ptmm) REVERT: A 472 GLU cc_start: 0.8958 (pm20) cc_final: 0.8244 (pm20) REVERT: A 473 ASP cc_start: 0.9207 (m-30) cc_final: 0.8972 (m-30) REVERT: A 488 ARG cc_start: 0.8187 (ttm-80) cc_final: 0.7645 (ttm-80) REVERT: A 492 ASP cc_start: 0.9139 (m-30) cc_final: 0.8657 (m-30) REVERT: A 500 GLU cc_start: 0.8431 (pm20) cc_final: 0.8063 (pm20) REVERT: A 513 LYS cc_start: 0.9028 (mmpt) cc_final: 0.8762 (mmmt) REVERT: B 489 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8215 (mp10) REVERT: B 492 ASP cc_start: 0.8978 (m-30) cc_final: 0.8608 (m-30) REVERT: B 495 ASP cc_start: 0.8061 (t70) cc_final: 0.7502 (t0) REVERT: B 503 LYS cc_start: 0.9245 (pttp) cc_final: 0.8885 (pttm) REVERT: C 461 ASP cc_start: 0.8965 (m-30) cc_final: 0.8532 (m-30) REVERT: C 470 MET cc_start: 0.8697 (mtp) cc_final: 0.8077 (mtm) REVERT: C 480 LYS cc_start: 0.8603 (ptpp) cc_final: 0.8333 (ptpp) REVERT: D 441 GLN cc_start: 0.8616 (tp-100) cc_final: 0.8154 (tm-30) REVERT: D 466 ARG cc_start: 0.8968 (mpp80) cc_final: 0.8711 (mpp80) REVERT: D 478 SER cc_start: 0.9549 (t) cc_final: 0.9306 (p) REVERT: D 480 LYS cc_start: 0.9097 (ttmm) cc_final: 0.8481 (ttmm) REVERT: D 486 LYS cc_start: 0.8986 (mttm) cc_final: 0.8744 (mmtm) REVERT: D 503 LYS cc_start: 0.8896 (pttm) cc_final: 0.8642 (pttm) REVERT: E 446 ASP cc_start: 0.9069 (m-30) cc_final: 0.8583 (p0) REVERT: E 461 ASP cc_start: 0.8582 (m-30) cc_final: 0.7231 (t70) REVERT: E 471 LYS cc_start: 0.8808 (mttt) cc_final: 0.8426 (pttt) REVERT: E 474 TYR cc_start: 0.9266 (t80) cc_final: 0.9063 (t80) REVERT: E 480 LYS cc_start: 0.9121 (mtpt) cc_final: 0.8526 (ttmm) REVERT: E 486 LYS cc_start: 0.9330 (mtpt) cc_final: 0.9095 (mttp) REVERT: E 489 GLN cc_start: 0.8709 (mp10) cc_final: 0.8282 (mp10) REVERT: E 501 PHE cc_start: 0.8698 (t80) cc_final: 0.8154 (t80) REVERT: E 503 LYS cc_start: 0.9344 (pttm) cc_final: 0.8988 (pttm) REVERT: F 449 ASN cc_start: 0.8520 (m110) cc_final: 0.8204 (p0) REVERT: F 460 LEU cc_start: 0.9306 (pp) cc_final: 0.8982 (pp) REVERT: F 470 MET cc_start: 0.6786 (ttt) cc_final: 0.6552 (mtm) REVERT: G 446 ASP cc_start: 0.8661 (m-30) cc_final: 0.8150 (m-30) REVERT: G 475 GLU cc_start: 0.7980 (mp0) cc_final: 0.6966 (tm-30) REVERT: G 503 LYS cc_start: 0.9346 (ptpp) cc_final: 0.9096 (pttp) REVERT: H 470 MET cc_start: 0.9044 (mpp) cc_final: 0.7757 (mpp) REVERT: H 489 GLN cc_start: 0.8646 (mp10) cc_final: 0.8391 (mp10) REVERT: H 501 PHE cc_start: 0.8709 (t80) cc_final: 0.8372 (t80) REVERT: H 507 GLN cc_start: 0.8991 (mp10) cc_final: 0.8732 (mp-120) REVERT: I 461 ASP cc_start: 0.9039 (t70) cc_final: 0.8181 (t70) REVERT: I 463 LEU cc_start: 0.9464 (mt) cc_final: 0.9217 (mt) REVERT: I 480 LYS cc_start: 0.8890 (mttp) cc_final: 0.8599 (mttp) REVERT: I 484 THR cc_start: 0.8519 (p) cc_final: 0.8016 (p) REVERT: I 489 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7950 (tm-30) REVERT: I 491 LEU cc_start: 0.9222 (mt) cc_final: 0.9021 (mt) REVERT: J 446 ASP cc_start: 0.9184 (p0) cc_final: 0.8614 (p0) REVERT: J 450 GLN cc_start: 0.8874 (mt0) cc_final: 0.8667 (mp10) REVERT: J 453 GLU cc_start: 0.9127 (tp30) cc_final: 0.8711 (tp30) REVERT: J 457 ASN cc_start: 0.9011 (p0) cc_final: 0.8369 (p0) REVERT: J 472 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8383 (mp0) REVERT: J 475 GLU cc_start: 0.9354 (mt-10) cc_final: 0.9000 (mt-10) REVERT: J 476 LEU cc_start: 0.9488 (mt) cc_final: 0.9273 (mt) REVERT: J 478 SER cc_start: 0.9547 (m) cc_final: 0.9240 (p) REVERT: J 480 LYS cc_start: 0.8952 (ptpp) cc_final: 0.8701 (ptpp) REVERT: J 488 ARG cc_start: 0.8098 (mtt-85) cc_final: 0.7886 (mtt180) REVERT: J 501 PHE cc_start: 0.9275 (t80) cc_final: 0.8929 (t80) REVERT: K 444 ARG cc_start: 0.7212 (ttm170) cc_final: 0.6288 (ptt-90) REVERT: K 449 ASN cc_start: 0.9227 (m110) cc_final: 0.9007 (m110) REVERT: K 471 LYS cc_start: 0.8934 (mmmm) cc_final: 0.8054 (ttpt) REVERT: K 476 LEU cc_start: 0.9238 (mt) cc_final: 0.9009 (mt) REVERT: K 503 LYS cc_start: 0.9308 (ptmm) cc_final: 0.8975 (ptpp) REVERT: L 441 GLN cc_start: 0.9115 (mt0) cc_final: 0.8718 (tm-30) REVERT: L 460 LEU cc_start: 0.9613 (mp) cc_final: 0.9377 (mp) REVERT: L 472 GLU cc_start: 0.8708 (pm20) cc_final: 0.7944 (pm20) REVERT: L 480 LYS cc_start: 0.7426 (pttm) cc_final: 0.7022 (pttm) REVERT: L 499 GLU cc_start: 0.8646 (pp20) cc_final: 0.8236 (pp20) REVERT: L 500 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8594 (mm-30) REVERT: L 503 LYS cc_start: 0.9429 (mtpp) cc_final: 0.8993 (mtpp) outliers start: 1 outliers final: 0 residues processed: 445 average time/residue: 0.1047 time to fit residues: 61.2286 Evaluate side-chains 368 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 367 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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: 1.9990 chunk 23 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 73 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 80 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN A 512 ASN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 GLN B 489 GLN ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 457 ASN ** F 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 437 GLN H 512 ASN I 512 ASN ** J 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 458 GLN ** K 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN L 449 ASN L 512 ASN L 514 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.068413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.055010 restraints weight = 37452.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.057051 restraints weight = 24952.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.058524 restraints weight = 18363.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.059678 restraints weight = 14458.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.060539 restraints weight = 11852.234| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 1.9298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8328 Z= 0.198 Angle : 0.837 8.162 11184 Z= 0.445 Chirality : 0.048 0.182 1332 Planarity : 0.005 0.069 1440 Dihedral : 5.537 28.689 1092 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 21.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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: -1.14 (0.25), residues: 1020 helix: -0.43 (0.16), residues: 888 sheet: None (None), residues: 0 loop : -1.95 (0.51), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 483 TYR 0.019 0.002 TYR H 474 PHE 0.012 0.002 PHE E 501 TRP 0.037 0.003 TRP I 439 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 8328) covalent geometry : angle 0.83744 (11184) hydrogen bonds : bond 0.03659 ( 529) hydrogen bonds : angle 4.90955 ( 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 461 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 461 time to evaluate : 0.352 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 445 GLU cc_start: 0.8923 (pm20) cc_final: 0.8616 (pm20) REVERT: A 450 GLN cc_start: 0.8948 (mt0) cc_final: 0.8702 (pt0) REVERT: A 461 ASP cc_start: 0.9126 (m-30) cc_final: 0.8913 (t70) REVERT: A 470 MET cc_start: 0.9027 (mtt) cc_final: 0.8333 (mtt) REVERT: A 471 LYS cc_start: 0.9170 (ptpp) cc_final: 0.8753 (ttpp) REVERT: A 472 GLU cc_start: 0.8968 (pm20) cc_final: 0.7986 (pm20) REVERT: A 473 ASP cc_start: 0.9195 (m-30) cc_final: 0.8855 (m-30) REVERT: A 488 ARG cc_start: 0.8389 (ttm-80) cc_final: 0.7865 (ttm-80) REVERT: A 492 ASP cc_start: 0.9218 (m-30) cc_final: 0.8794 (m-30) REVERT: A 500 GLU cc_start: 0.8510 (pm20) cc_final: 0.8058 (pm20) REVERT: A 513 LYS cc_start: 0.9044 (mmpt) cc_final: 0.8782 (mmmt) REVERT: B 492 ASP cc_start: 0.8943 (m-30) cc_final: 0.8426 (m-30) REVERT: B 495 ASP cc_start: 0.8056 (t70) cc_final: 0.7551 (t0) REVERT: B 499 GLU cc_start: 0.8679 (mt-10) cc_final: 0.7878 (mm-30) REVERT: C 450 GLN cc_start: 0.7347 (mt0) cc_final: 0.6210 (tm-30) REVERT: C 461 ASP cc_start: 0.9006 (m-30) cc_final: 0.8487 (m-30) REVERT: C 470 MET cc_start: 0.8633 (mtp) cc_final: 0.8174 (mtm) REVERT: C 491 LEU cc_start: 0.9424 (mt) cc_final: 0.9110 (mp) REVERT: C 495 ASP cc_start: 0.8832 (m-30) cc_final: 0.8508 (m-30) REVERT: D 441 GLN cc_start: 0.8648 (tp-100) cc_final: 0.8188 (tm-30) REVERT: D 466 ARG cc_start: 0.9058 (mpp80) cc_final: 0.8780 (mpp80) REVERT: D 472 GLU cc_start: 0.8630 (tt0) cc_final: 0.8339 (tt0) REVERT: D 478 SER cc_start: 0.9631 (t) cc_final: 0.9349 (p) REVERT: E 446 ASP cc_start: 0.9221 (m-30) cc_final: 0.8747 (p0) REVERT: E 461 ASP cc_start: 0.8863 (m-30) cc_final: 0.7467 (t70) REVERT: E 471 LYS cc_start: 0.8787 (mttt) cc_final: 0.8533 (pttt) REVERT: E 474 TYR cc_start: 0.9321 (t80) cc_final: 0.9021 (t80) REVERT: E 476 LEU cc_start: 0.9162 (mt) cc_final: 0.8476 (mt) REVERT: E 480 LYS cc_start: 0.9106 (mtpt) cc_final: 0.8649 (ttmm) REVERT: E 489 GLN cc_start: 0.8722 (mp10) cc_final: 0.8273 (mp10) REVERT: E 501 PHE cc_start: 0.8686 (t80) cc_final: 0.8148 (t80) REVERT: E 503 LYS cc_start: 0.9342 (pttm) cc_final: 0.9009 (pttm) REVERT: F 441 GLN cc_start: 0.8250 (tp-100) cc_final: 0.7893 (tp40) REVERT: F 446 ASP cc_start: 0.9149 (t70) cc_final: 0.8855 (t0) REVERT: F 456 LEU cc_start: 0.9456 (tp) cc_final: 0.9214 (tp) REVERT: F 460 LEU cc_start: 0.9452 (pp) cc_final: 0.9142 (pp) REVERT: F 470 MET cc_start: 0.7751 (ttt) cc_final: 0.7372 (mtm) REVERT: G 461 ASP cc_start: 0.9294 (m-30) cc_final: 0.8458 (t0) REVERT: G 464 LEU cc_start: 0.9340 (mt) cc_final: 0.9131 (mt) REVERT: G 475 GLU cc_start: 0.7787 (mp0) cc_final: 0.7120 (tm-30) REVERT: G 515 MET cc_start: 0.2807 (mmp) cc_final: 0.2439 (mmp) REVERT: H 453 GLU cc_start: 0.8597 (tm-30) cc_final: 0.7804 (tm-30) REVERT: H 470 MET cc_start: 0.9022 (mpp) cc_final: 0.7768 (mtm) REVERT: H 478 SER cc_start: 0.9424 (m) cc_final: 0.9187 (p) REVERT: H 489 GLN cc_start: 0.8560 (mp10) cc_final: 0.8231 (mp10) REVERT: H 492 ASP cc_start: 0.9201 (m-30) cc_final: 0.8929 (m-30) REVERT: H 500 GLU cc_start: 0.8201 (mp0) cc_final: 0.7771 (pm20) REVERT: H 501 PHE cc_start: 0.8588 (t80) cc_final: 0.8221 (t80) REVERT: I 463 LEU cc_start: 0.9407 (mt) cc_final: 0.9159 (mt) REVERT: I 478 SER cc_start: 0.9642 (t) cc_final: 0.9441 (p) REVERT: I 484 THR cc_start: 0.8878 (p) cc_final: 0.8510 (p) REVERT: I 491 LEU cc_start: 0.9349 (mt) cc_final: 0.9093 (mt) REVERT: I 495 ASP cc_start: 0.9239 (m-30) cc_final: 0.8977 (m-30) REVERT: J 441 GLN cc_start: 0.8002 (tm-30) cc_final: 0.7525 (tm-30) REVERT: J 453 GLU cc_start: 0.9316 (tp30) cc_final: 0.9070 (tp30) REVERT: J 475 GLU cc_start: 0.9302 (mt-10) cc_final: 0.8944 (mt-10) REVERT: J 478 SER cc_start: 0.9532 (m) cc_final: 0.9226 (p) REVERT: J 480 LYS cc_start: 0.8891 (ptpp) cc_final: 0.8590 (ptpp) REVERT: K 444 ARG cc_start: 0.7425 (ttm170) cc_final: 0.6769 (ptt180) REVERT: K 449 ASN cc_start: 0.9368 (m110) cc_final: 0.8999 (m110) REVERT: K 461 ASP cc_start: 0.9038 (m-30) cc_final: 0.8677 (m-30) REVERT: K 470 MET cc_start: 0.6063 (mtm) cc_final: 0.5731 (mtt) REVERT: K 471 LYS cc_start: 0.9100 (mmmm) cc_final: 0.8444 (ttpt) REVERT: K 476 LEU cc_start: 0.9309 (mt) cc_final: 0.9045 (mt) REVERT: K 503 LYS cc_start: 0.9128 (ptmm) cc_final: 0.8525 (ptmm) REVERT: L 440 ILE cc_start: 0.9738 (mm) cc_final: 0.9534 (mm) REVERT: L 441 GLN cc_start: 0.9104 (mt0) cc_final: 0.8797 (mm-40) REVERT: L 460 LEU cc_start: 0.9610 (mp) cc_final: 0.9334 (mp) REVERT: L 472 GLU cc_start: 0.8763 (pm20) cc_final: 0.8223 (pm20) REVERT: L 476 LEU cc_start: 0.9281 (mt) cc_final: 0.9072 (mt) REVERT: L 480 LYS cc_start: 0.7221 (pttm) cc_final: 0.6940 (pttm) REVERT: L 491 LEU cc_start: 0.9650 (mm) cc_final: 0.9446 (mp) outliers start: 0 outliers final: 0 residues processed: 461 average time/residue: 0.1058 time to fit residues: 64.3682 Evaluate side-chains 383 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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: 1.9990 chunk 91 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 8 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 56 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN A 512 ASN ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 512 ASN I 512 ASN ** J 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 458 GLN ** K 489 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 = 0.3363 r_free = 0.3363 target = 0.067096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.053510 restraints weight = 37251.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.055425 restraints weight = 24512.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.056908 restraints weight = 18126.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.058001 restraints weight = 14247.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.058855 restraints weight = 11786.215| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 1.9653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8328 Z= 0.173 Angle : 0.839 7.830 11184 Z= 0.441 Chirality : 0.048 0.237 1332 Planarity : 0.005 0.105 1440 Dihedral : 5.529 28.102 1092 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % 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: -1.05 (0.25), residues: 1020 helix: -0.36 (0.16), residues: 888 sheet: None (None), residues: 0 loop : -2.03 (0.51), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 483 TYR 0.015 0.002 TYR H 474 PHE 0.010 0.002 PHE E 501 TRP 0.038 0.003 TRP I 439 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 8328) covalent geometry : angle 0.83914 (11184) hydrogen bonds : bond 0.03549 ( 529) hydrogen bonds : angle 4.96182 ( 1587) =============================================================================== Job complete usr+sys time: 1621.69 seconds wall clock time: 28 minutes 57.50 seconds (1737.50 seconds total)