Starting phenix.real_space_refine on Wed Mar 12 14:45:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5yrn_6842/03_2025/5yrn_6842.cif Found real_map, /net/cci-nas-00/data/ceres_data/5yrn_6842/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5yrn_6842/03_2025/5yrn_6842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5yrn_6842/03_2025/5yrn_6842.map" model { file = "/net/cci-nas-00/data/ceres_data/5yrn_6842/03_2025/5yrn_6842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5yrn_6842/03_2025/5yrn_6842.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 2.67, per 1000 atoms: 0.32 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: 1.97 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.76 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: 2.17 Time building geometry restraints manager: 2.35 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' 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: 0.330 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 20.810 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.850 ------------------------------------------------------------------------------- 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= 0.446 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (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 TRP 0.020 0.004 TRP I 439 PHE 0.007 0.003 PHE K 501 TYR 0.003 0.001 TYR B 474 ARG 0.011 0.002 ARG L 444 *********************** 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 : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 487 VAL cc_start: 0.7278 (t) cc_final: 0.6776 (t) REVERT: B 503 LYS cc_start: 0.8979 (ttmt) cc_final: 0.8663 (tptt) REVERT: C 447 ILE cc_start: 0.7579 (mt) cc_final: 0.6532 (mt) REVERT: C 470 MET cc_start: 0.4199 (mtm) cc_final: 0.3701 (mtt) REVERT: C 488 ARG cc_start: 0.6586 (mtt-85) cc_final: 0.6309 (tpp-160) REVERT: E 500 GLU cc_start: 0.8194 (tt0) cc_final: 0.7845 (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: 0.7531 (tp) REVERT: H 471 LYS cc_start: 0.7596 (tttt) cc_final: 0.7162 (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: 0.7373 (tm-30) REVERT: L 460 LEU cc_start: 0.8505 (mt) cc_final: 0.8244 (mt) REVERT: L 470 MET cc_start: 0.7397 (mtm) cc_final: 0.7024 (mpp) REVERT: L 480 LYS cc_start: 0.7864 (mmtt) cc_final: 0.7548 (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: 0.3085 time to fit residues: 157.9043 Evaluate side-chains 217 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 56 optimal weight: 20.0000 chunk 87 optimal weight: 0.5980 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 GLN B 497 GLN ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** G 514 GLN H 497 GLN H 514 GLN I 458 GLN K 514 GLN L 512 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.085611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.069884 restraints weight = 32969.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.072158 restraints weight = 22793.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.073894 restraints weight = 17205.570| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.7764 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= 0.284 Angle : 0.768 10.166 11184 Z= 0.408 Chirality : 0.044 0.216 1332 Planarity : 0.006 0.123 1440 Dihedral : 5.631 22.536 1092 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.22), residues: 1020 helix: -1.27 (0.14), residues: 900 sheet: None (None), residues: 0 loop : -0.96 (0.49), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 439 PHE 0.011 0.003 PHE I 501 TYR 0.009 0.002 TYR B 474 ARG 0.012 0.002 ARG J 483 *********************** 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 347 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 LYS cc_start: 0.7913 (ptmm) cc_final: 0.7442 (pmmt) REVERT: A 448 VAL cc_start: 0.8531 (t) cc_final: 0.8116 (p) REVERT: A 492 ASP cc_start: 0.8369 (m-30) cc_final: 0.8029 (m-30) REVERT: A 494 THR cc_start: 0.9246 (m) cc_final: 0.9020 (m) REVERT: A 509 LEU cc_start: 0.9178 (mm) cc_final: 0.8919 (mm) REVERT: B 460 LEU cc_start: 0.7468 (mt) cc_final: 0.7182 (mt) REVERT: B 503 LYS cc_start: 0.9176 (ttmt) cc_final: 0.8851 (tptt) REVERT: C 479 THR cc_start: 0.6230 (m) cc_final: 0.5801 (m) REVERT: C 480 LYS cc_start: 0.8519 (mppt) cc_final: 0.8277 (mttp) REVERT: C 503 LYS cc_start: 0.8380 (ttmt) cc_final: 0.7896 (tptt) REVERT: C 513 LYS cc_start: 0.8376 (mmmt) cc_final: 0.8028 (tppt) REVERT: D 480 LYS cc_start: 0.8885 (mttp) cc_final: 0.8631 (mtpp) REVERT: D 488 ARG cc_start: 0.8366 (mmm-85) cc_final: 0.8163 (mmm160) REVERT: D 513 LYS cc_start: 0.8600 (pptt) cc_final: 0.8088 (tptp) REVERT: E 461 ASP cc_start: 0.8882 (m-30) cc_final: 0.8427 (t70) REVERT: E 470 MET cc_start: 0.6786 (ptp) cc_final: 0.6522 (ptp) REVERT: E 480 LYS cc_start: 0.8306 (mtpt) cc_final: 0.8000 (ttmt) REVERT: E 483 ARG cc_start: 0.7529 (mtt180) cc_final: 0.7077 (ttm-80) REVERT: F 450 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7565 (mt0) REVERT: G 440 ILE cc_start: 0.9082 (mm) cc_final: 0.8831 (mt) REVERT: G 475 GLU cc_start: 0.7564 (mp0) cc_final: 0.7069 (mt-10) REVERT: H 471 LYS cc_start: 0.7986 (tttt) cc_final: 0.7704 (pttt) REVERT: H 477 VAL cc_start: 0.7043 (t) cc_final: 0.5443 (p) REVERT: J 435 ILE cc_start: 0.7539 (mt) cc_final: 0.6879 (tp) REVERT: J 443 LYS cc_start: 0.7211 (ptmm) cc_final: 0.6820 (ptmm) REVERT: J 445 GLU cc_start: 0.7444 (mp0) cc_final: 0.6577 (mp0) REVERT: J 446 ASP cc_start: 0.8512 (t0) cc_final: 0.8093 (t0) REVERT: J 499 GLU cc_start: 0.8119 (pp20) cc_final: 0.7815 (tm-30) REVERT: J 501 PHE cc_start: 0.7583 (t80) cc_final: 0.7350 (t80) REVERT: L 430 THR cc_start: 0.8286 (p) cc_final: 0.7962 (t) REVERT: L 453 GLU cc_start: 0.8414 (tm-30) cc_final: 0.7814 (tm-30) REVERT: L 509 LEU cc_start: 0.9153 (tt) cc_final: 0.8833 (pp) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.2620 time to fit residues: 114.6512 Evaluate side-chains 247 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 88 optimal weight: 20.0000 chunk 94 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN B 458 GLN B 497 GLN ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN E 497 GLN E 512 ASN F 437 GLN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 ASN H 457 ASN ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN L 512 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.082440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.067289 restraints weight = 33038.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.069614 restraints weight = 22627.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.071401 restraints weight = 16834.496| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 1.0392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8328 Z= 0.213 Angle : 0.662 7.901 11184 Z= 0.358 Chirality : 0.042 0.358 1332 Planarity : 0.004 0.053 1440 Dihedral : 5.142 24.026 1092 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.24), residues: 1020 helix: -0.59 (0.15), residues: 924 sheet: None (None), residues: 0 loop : -1.07 (0.58), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 439 PHE 0.013 0.003 PHE D 501 TYR 0.012 0.002 TYR J 474 ARG 0.010 0.001 ARG J 483 *********************** 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 375 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 0.933 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: A 448 VAL cc_start: 0.8707 (t) cc_final: 0.8487 (p) REVERT: A 461 ASP cc_start: 0.9090 (m-30) cc_final: 0.8783 (m-30) REVERT: A 471 LYS cc_start: 0.9082 (ptpp) cc_final: 0.8836 (ptmm) REVERT: A 484 THR cc_start: 0.9324 (p) cc_final: 0.9111 (p) REVERT: A 492 ASP cc_start: 0.8902 (m-30) cc_final: 0.8696 (m-30) REVERT: B 458 GLN cc_start: 0.8862 (mp10) cc_final: 0.8652 (mp10) REVERT: B 470 MET cc_start: 0.8103 (mtm) cc_final: 0.7775 (mtt) REVERT: B 503 LYS cc_start: 0.9151 (ttmt) cc_final: 0.8892 (tptt) REVERT: C 447 ILE cc_start: 0.7459 (mt) cc_final: 0.7200 (mt) REVERT: C 461 ASP cc_start: 0.7789 (m-30) cc_final: 0.7320 (m-30) REVERT: D 450 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7315 (mt0) REVERT: D 470 MET cc_start: 0.7520 (ptp) cc_final: 0.7186 (ptt) REVERT: D 480 LYS cc_start: 0.8865 (mttp) cc_final: 0.8538 (ttmm) REVERT: D 483 ARG cc_start: 0.7965 (mtt180) cc_final: 0.7176 (mtp-110) REVERT: D 507 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8640 (tp-100) REVERT: D 513 LYS cc_start: 0.8584 (pptt) cc_final: 0.8335 (mmmt) REVERT: E 461 ASP cc_start: 0.9101 (m-30) cc_final: 0.8289 (t70) REVERT: E 473 ASP cc_start: 0.7851 (m-30) cc_final: 0.7401 (m-30) REVERT: E 483 ARG cc_start: 0.7855 (mtt180) cc_final: 0.7285 (ttm-80) REVERT: E 503 LYS cc_start: 0.9483 (pttm) cc_final: 0.9234 (pttm) REVERT: F 445 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6804 (mp0) REVERT: F 515 MET cc_start: 0.7092 (tpt) cc_final: 0.6861 (tpt) REVERT: G 475 GLU cc_start: 0.7617 (mp0) cc_final: 0.6779 (pt0) REVERT: H 438 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8459 (pp30) REVERT: H 453 GLU cc_start: 0.8891 (pm20) cc_final: 0.8578 (pm20) REVERT: H 470 MET cc_start: 0.7241 (mpp) cc_final: 0.5576 (mpp) REVERT: H 473 ASP cc_start: 0.6915 (m-30) cc_final: 0.6448 (m-30) REVERT: H 477 VAL cc_start: 0.7180 (t) cc_final: 0.6537 (p) REVERT: I 477 VAL cc_start: 0.6078 (t) cc_final: 0.4801 (m) REVERT: I 480 LYS cc_start: 0.9145 (mmtt) cc_final: 0.8851 (mmmm) REVERT: I 482 THR cc_start: 0.8522 (p) cc_final: 0.7596 (p) REVERT: I 483 ARG cc_start: 0.7888 (mmp80) cc_final: 0.7348 (mtp-110) REVERT: I 515 MET cc_start: 0.6104 (tpp) cc_final: 0.5541 (tpp) REVERT: J 445 GLU cc_start: 0.7641 (mp0) cc_final: 0.6889 (mp0) REVERT: J 449 ASN cc_start: 0.9012 (m-40) cc_final: 0.8634 (m-40) REVERT: J 499 GLU cc_start: 0.8204 (pp20) cc_final: 0.7922 (tm-30) REVERT: J 501 PHE cc_start: 0.8411 (t80) cc_final: 0.7842 (t80) REVERT: J 503 LYS cc_start: 0.8459 (pptt) cc_final: 0.8236 (pttm) REVERT: K 480 LYS cc_start: 0.6814 (mmtt) cc_final: 0.6492 (mmtt) REVERT: L 453 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7594 (tm-30) REVERT: L 457 ASN cc_start: 0.8502 (p0) cc_final: 0.7755 (p0) REVERT: L 476 LEU cc_start: 0.8896 (mt) cc_final: 0.8668 (mt) REVERT: L 489 GLN cc_start: 0.9059 (mm110) cc_final: 0.8254 (tp40) REVERT: L 496 ILE cc_start: 0.8362 (pt) cc_final: 0.7627 (mp) REVERT: L 509 LEU cc_start: 0.9209 (tt) cc_final: 0.8984 (pp) outliers start: 0 outliers final: 0 residues processed: 375 average time/residue: 0.2898 time to fit residues: 140.0463 Evaluate side-chains 274 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 30.0000 chunk 92 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 64 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 88 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 437 GLN C 449 ASN C 458 GLN ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 457 ASN E 512 ASN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 ASN H 437 GLN H 512 ASN ** I 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 438 GLN J 497 GLN L 497 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 = 0.3499 r_free = 0.3499 target = 0.076043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.062037 restraints weight = 35420.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.064244 restraints weight = 23867.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.065942 restraints weight = 17599.334| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 1.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 8328 Z= 0.311 Angle : 0.796 8.763 11184 Z= 0.424 Chirality : 0.044 0.235 1332 Planarity : 0.005 0.058 1440 Dihedral : 5.531 21.223 1092 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.24), residues: 1020 helix: -0.39 (0.16), residues: 888 sheet: None (None), residues: 0 loop : -1.35 (0.49), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP K 439 PHE 0.024 0.004 PHE G 501 TYR 0.019 0.002 TYR G 474 ARG 0.010 0.001 ARG J 483 *********************** 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 448 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 448 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 LEU cc_start: 0.9660 (tp) cc_final: 0.9438 (mt) REVERT: A 468 LEU cc_start: 0.9240 (mp) cc_final: 0.8985 (mm) REVERT: A 471 LYS cc_start: 0.9103 (ptpp) cc_final: 0.8668 (ptmm) REVERT: A 472 GLU cc_start: 0.9159 (mp0) cc_final: 0.8938 (mp0) REVERT: A 489 GLN cc_start: 0.8405 (tm-30) cc_final: 0.8176 (tp40) REVERT: A 513 LYS cc_start: 0.9090 (mmpt) cc_final: 0.8861 (mmmt) REVERT: B 448 VAL cc_start: 0.6611 (t) cc_final: 0.6398 (t) REVERT: B 458 GLN cc_start: 0.9111 (mp10) cc_final: 0.8889 (pt0) REVERT: B 460 LEU cc_start: 0.9217 (mt) cc_final: 0.8903 (mt) REVERT: B 468 LEU cc_start: 0.9344 (mt) cc_final: 0.9139 (mt) REVERT: B 470 MET cc_start: 0.8584 (mtm) cc_final: 0.7745 (mtt) REVERT: B 500 GLU cc_start: 0.8555 (tt0) cc_final: 0.8063 (pm20) REVERT: C 440 ILE cc_start: 0.8838 (mt) cc_final: 0.8602 (mt) REVERT: C 470 MET cc_start: 0.8638 (mtm) cc_final: 0.8178 (mtm) REVERT: C 478 SER cc_start: 0.9284 (t) cc_final: 0.9043 (p) REVERT: C 513 LYS cc_start: 0.8642 (mmmt) cc_final: 0.8367 (mmmt) REVERT: C 515 MET cc_start: 0.6190 (tpt) cc_final: 0.5541 (mmt) REVERT: D 440 ILE cc_start: 0.9067 (mt) cc_final: 0.8822 (mt) REVERT: D 470 MET cc_start: 0.8365 (ptp) cc_final: 0.8134 (ptp) REVERT: D 471 LYS cc_start: 0.9371 (tptp) cc_final: 0.9116 (tmtt) REVERT: D 483 ARG cc_start: 0.8577 (mtt180) cc_final: 0.7968 (ttp80) REVERT: D 507 GLN cc_start: 0.9279 (tm-30) cc_final: 0.8817 (tp-100) REVERT: E 438 GLN cc_start: 0.9370 (pp30) cc_final: 0.9148 (pp30) REVERT: E 446 ASP cc_start: 0.9239 (m-30) cc_final: 0.8995 (m-30) REVERT: E 461 ASP cc_start: 0.8593 (m-30) cc_final: 0.7568 (t70) REVERT: E 471 LYS cc_start: 0.8774 (tttt) cc_final: 0.8090 (tmtt) REVERT: E 473 ASP cc_start: 0.8157 (m-30) cc_final: 0.7870 (m-30) REVERT: E 480 LYS cc_start: 0.8960 (mtpt) cc_final: 0.8522 (ttmm) REVERT: E 483 ARG cc_start: 0.8553 (mtt180) cc_final: 0.8135 (ttm170) REVERT: E 489 GLN cc_start: 0.8773 (mp10) cc_final: 0.8556 (mp10) REVERT: F 450 GLN cc_start: 0.8435 (mm110) cc_final: 0.8042 (mm-40) REVERT: F 458 GLN cc_start: 0.9452 (mm110) cc_final: 0.8675 (pt0) REVERT: F 461 ASP cc_start: 0.8776 (t70) cc_final: 0.7655 (t70) REVERT: G 446 ASP cc_start: 0.8663 (m-30) cc_final: 0.8017 (m-30) REVERT: G 457 ASN cc_start: 0.8821 (m110) cc_final: 0.8581 (m110) REVERT: G 461 ASP cc_start: 0.8538 (m-30) cc_final: 0.8281 (m-30) REVERT: G 475 GLU cc_start: 0.7938 (mp0) cc_final: 0.7296 (tp30) REVERT: G 501 PHE cc_start: 0.7482 (t80) cc_final: 0.6235 (t80) REVERT: H 441 GLN cc_start: 0.8971 (pp30) cc_final: 0.8564 (pp30) REVERT: H 443 LYS cc_start: 0.9053 (mttt) cc_final: 0.8497 (mtmm) REVERT: H 470 MET cc_start: 0.8178 (mpp) cc_final: 0.7278 (mpp) REVERT: H 501 PHE cc_start: 0.8386 (t80) cc_final: 0.8005 (t80) REVERT: I 447 ILE cc_start: 0.8267 (mt) cc_final: 0.7956 (mm) REVERT: I 461 ASP cc_start: 0.8392 (t70) cc_final: 0.7722 (t70) REVERT: I 475 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8212 (tt0) REVERT: I 482 THR cc_start: 0.9179 (p) cc_final: 0.8063 (p) REVERT: I 503 LYS cc_start: 0.8935 (pttp) cc_final: 0.8576 (pttp) REVERT: I 515 MET cc_start: 0.6880 (tpp) cc_final: 0.5984 (mmm) REVERT: J 445 GLU cc_start: 0.8471 (mp0) cc_final: 0.7762 (mp0) REVERT: J 448 VAL cc_start: 0.9317 (t) cc_final: 0.9028 (m) REVERT: J 449 ASN cc_start: 0.9341 (m-40) cc_final: 0.8837 (m-40) REVERT: J 470 MET cc_start: 0.7936 (mtt) cc_final: 0.7563 (mpp) REVERT: J 474 TYR cc_start: 0.9352 (t80) cc_final: 0.8922 (t80) REVERT: J 476 LEU cc_start: 0.9586 (mt) cc_final: 0.9383 (mt) REVERT: J 492 ASP cc_start: 0.9308 (m-30) cc_final: 0.9087 (m-30) REVERT: J 501 PHE cc_start: 0.8824 (t80) cc_final: 0.8574 (t80) REVERT: K 444 ARG cc_start: 0.6711 (ttm170) cc_final: 0.6181 (ptt-90) REVERT: K 451 MET cc_start: 0.8767 (tpt) cc_final: 0.8445 (tpp) REVERT: K 453 GLU cc_start: 0.9091 (tm-30) cc_final: 0.8788 (tp30) REVERT: K 456 LEU cc_start: 0.8901 (tp) cc_final: 0.8559 (tp) REVERT: K 464 LEU cc_start: 0.9049 (tt) cc_final: 0.8773 (mp) REVERT: K 508 LYS cc_start: 0.7041 (tptp) cc_final: 0.6565 (tttm) REVERT: L 475 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7778 (mt-10) REVERT: L 476 LEU cc_start: 0.9183 (mt) cc_final: 0.8978 (mt) REVERT: L 489 GLN cc_start: 0.9226 (mm110) cc_final: 0.8573 (tp-100) REVERT: L 492 ASP cc_start: 0.9342 (m-30) cc_final: 0.8943 (m-30) outliers start: 0 outliers final: 0 residues processed: 448 average time/residue: 0.2499 time to fit residues: 142.6519 Evaluate side-chains 335 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 29 optimal weight: 6.9990 chunk 64 optimal weight: 30.0000 chunk 63 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 8 optimal weight: 20.0000 chunk 65 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 457 ASN ** E 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 512 ASN ** F 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 ASN H 512 ASN ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 438 GLN K 512 ASN L 497 GLN L 512 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.067775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.053914 restraints weight = 37624.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.055825 restraints weight = 25440.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.057278 restraints weight = 18988.385| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 1.7550 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= 0.336 Angle : 0.816 8.516 11184 Z= 0.439 Chirality : 0.046 0.226 1332 Planarity : 0.006 0.070 1440 Dihedral : 5.772 27.815 1092 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 21.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.11 % Allowed : 4.11 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.24), residues: 1020 helix: -0.57 (0.16), residues: 888 sheet: None (None), residues: 0 loop : -1.68 (0.48), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 439 PHE 0.018 0.003 PHE H 501 TYR 0.025 0.002 TYR H 474 ARG 0.009 0.001 ARG C 488 *********************** 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 482 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 481 time to evaluate : 1.044 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 461 ASP cc_start: 0.9210 (m-30) cc_final: 0.8997 (t70) REVERT: A 471 LYS cc_start: 0.9097 (ptpp) cc_final: 0.8560 (ttpp) REVERT: A 480 LYS cc_start: 0.9520 (mmtm) cc_final: 0.9200 (mmmt) REVERT: A 500 GLU cc_start: 0.8534 (pm20) cc_final: 0.7902 (pm20) REVERT: A 513 LYS cc_start: 0.9086 (mmpt) cc_final: 0.8854 (mmmt) REVERT: B 489 GLN cc_start: 0.8556 (mp10) cc_final: 0.8312 (mp10) REVERT: B 492 ASP cc_start: 0.8939 (m-30) cc_final: 0.8590 (m-30) REVERT: B 495 ASP cc_start: 0.8397 (t70) cc_final: 0.7941 (t0) REVERT: B 513 LYS cc_start: 0.9225 (pptt) cc_final: 0.8672 (mmmt) REVERT: C 459 SER cc_start: 0.9792 (m) cc_final: 0.9591 (p) REVERT: C 470 MET cc_start: 0.8917 (mtm) cc_final: 0.8430 (mtm) REVERT: C 473 ASP cc_start: 0.9345 (m-30) cc_final: 0.9080 (m-30) REVERT: C 478 SER cc_start: 0.9512 (t) cc_final: 0.9234 (p) REVERT: C 491 LEU cc_start: 0.8970 (mp) cc_final: 0.8321 (tt) REVERT: C 492 ASP cc_start: 0.9182 (m-30) cc_final: 0.8898 (m-30) REVERT: C 513 LYS cc_start: 0.8865 (mmmt) cc_final: 0.8644 (tppt) REVERT: D 446 ASP cc_start: 0.9116 (m-30) cc_final: 0.8809 (p0) REVERT: D 447 ILE cc_start: 0.9234 (mt) cc_final: 0.8979 (mt) REVERT: D 458 GLN cc_start: 0.9018 (mp10) cc_final: 0.8760 (pt0) REVERT: D 474 TYR cc_start: 0.9133 (t80) cc_final: 0.8904 (t80) REVERT: D 476 LEU cc_start: 0.9170 (mt) cc_final: 0.8964 (mt) REVERT: D 478 SER cc_start: 0.9443 (t) cc_final: 0.9193 (p) REVERT: D 483 ARG cc_start: 0.8949 (mtt180) cc_final: 0.8723 (ttp80) REVERT: D 503 LYS cc_start: 0.9015 (pttm) cc_final: 0.8714 (pttm) REVERT: E 443 LYS cc_start: 0.9383 (ptpt) cc_final: 0.9007 (ptpp) REVERT: E 445 GLU cc_start: 0.9002 (pm20) cc_final: 0.8640 (pm20) REVERT: E 446 ASP cc_start: 0.9314 (m-30) cc_final: 0.8762 (m-30) REVERT: E 461 ASP cc_start: 0.8853 (m-30) cc_final: 0.7615 (t70) REVERT: E 471 LYS cc_start: 0.8965 (tttt) cc_final: 0.8310 (tmtt) REVERT: E 480 LYS cc_start: 0.8651 (mtpt) cc_final: 0.7531 (ttmm) REVERT: E 483 ARG cc_start: 0.9034 (mtt180) cc_final: 0.8763 (ttm170) REVERT: E 486 LYS cc_start: 0.9344 (mtpp) cc_final: 0.8900 (mttp) REVERT: E 489 GLN cc_start: 0.9005 (mp10) cc_final: 0.8577 (mp10) REVERT: F 450 GLN cc_start: 0.8604 (mm110) cc_final: 0.8316 (mm-40) REVERT: G 461 ASP cc_start: 0.9256 (m-30) cc_final: 0.8386 (t70) REVERT: G 467 ASP cc_start: 0.8864 (t70) cc_final: 0.8663 (t70) REVERT: G 475 GLU cc_start: 0.7751 (mp0) cc_final: 0.6873 (tp30) REVERT: G 506 VAL cc_start: 0.9416 (t) cc_final: 0.9147 (t) REVERT: H 443 LYS cc_start: 0.9236 (mttt) cc_final: 0.9015 (mtmm) REVERT: H 470 MET cc_start: 0.9057 (mpp) cc_final: 0.7825 (mpp) REVERT: H 472 GLU cc_start: 0.8860 (tt0) cc_final: 0.8615 (tt0) REVERT: H 480 LYS cc_start: 0.8808 (ptmt) cc_final: 0.8452 (ptpp) REVERT: H 486 LYS cc_start: 0.9333 (mtpt) cc_final: 0.9030 (mttm) REVERT: H 496 ILE cc_start: 0.7860 (mm) cc_final: 0.7374 (tp) REVERT: H 500 GLU cc_start: 0.8339 (mp0) cc_final: 0.7929 (pm20) REVERT: H 501 PHE cc_start: 0.8845 (t80) cc_final: 0.8369 (t80) REVERT: H 515 MET cc_start: 0.3314 (mmp) cc_final: 0.2464 (tpp) REVERT: I 456 LEU cc_start: 0.9569 (tp) cc_final: 0.9332 (tp) REVERT: I 478 SER cc_start: 0.9629 (t) cc_final: 0.9412 (p) REVERT: I 479 THR cc_start: 0.8933 (m) cc_final: 0.8706 (p) REVERT: I 480 LYS cc_start: 0.9348 (mmtm) cc_final: 0.9035 (mmtm) REVERT: I 484 THR cc_start: 0.9396 (p) cc_final: 0.9111 (p) REVERT: I 491 LEU cc_start: 0.9252 (mp) cc_final: 0.9028 (mt) REVERT: I 503 LYS cc_start: 0.9238 (pttp) cc_final: 0.8920 (pttp) REVERT: J 430 THR cc_start: 0.7825 (m) cc_final: 0.7597 (t) REVERT: J 445 GLU cc_start: 0.8656 (mp0) cc_final: 0.7943 (mp0) REVERT: J 449 ASN cc_start: 0.9361 (m-40) cc_final: 0.9023 (m-40) REVERT: J 451 MET cc_start: 0.8496 (tpp) cc_final: 0.8283 (tpp) REVERT: J 453 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8391 (tm-30) REVERT: J 470 MET cc_start: 0.8448 (mtt) cc_final: 0.8110 (mtt) REVERT: K 444 ARG cc_start: 0.7034 (ttm170) cc_final: 0.6567 (ptt-90) REVERT: K 446 ASP cc_start: 0.8406 (t0) cc_final: 0.8048 (t0) REVERT: K 449 ASN cc_start: 0.9412 (m-40) cc_final: 0.9163 (p0) REVERT: K 450 GLN cc_start: 0.8966 (mm-40) cc_final: 0.8617 (mm-40) REVERT: K 456 LEU cc_start: 0.9578 (tp) cc_final: 0.9359 (tp) REVERT: K 476 LEU cc_start: 0.9205 (mt) cc_final: 0.8940 (mt) REVERT: K 478 SER cc_start: 0.9331 (t) cc_final: 0.9046 (p) REVERT: L 441 GLN cc_start: 0.9253 (mt0) cc_final: 0.8890 (tm-30) REVERT: L 445 GLU cc_start: 0.8829 (pm20) cc_final: 0.8564 (pm20) REVERT: L 460 LEU cc_start: 0.9513 (mp) cc_final: 0.9255 (mp) REVERT: L 472 GLU cc_start: 0.8134 (tt0) cc_final: 0.7861 (tt0) REVERT: L 476 LEU cc_start: 0.9382 (mt) cc_final: 0.9181 (mt) REVERT: L 480 LYS cc_start: 0.9467 (mmtm) cc_final: 0.9101 (mmmm) REVERT: L 486 LYS cc_start: 0.9366 (mtpp) cc_final: 0.9071 (mtpp) REVERT: L 501 PHE cc_start: 0.8885 (t80) cc_final: 0.8621 (t80) outliers start: 1 outliers final: 1 residues processed: 482 average time/residue: 0.2255 time to fit residues: 141.2537 Evaluate side-chains 382 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 381 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 70 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 chunk 27 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 489 GLN ** C 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN D 450 GLN D 457 ASN ** D 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 GLN E 438 GLN E 450 GLN E 507 GLN F 441 GLN F 449 ASN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 512 ASN ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 438 GLN J 458 GLN ** J 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 449 ASN K 512 ASN K 514 GLN L 450 GLN ** L 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 512 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.068471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.053876 restraints weight = 37485.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.055818 restraints weight = 25520.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.057305 restraints weight = 19238.618| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 1.8105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 8328 Z= 0.239 Angle : 0.726 8.127 11184 Z= 0.391 Chirality : 0.043 0.193 1332 Planarity : 0.004 0.079 1440 Dihedral : 5.279 30.171 1092 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.32 % Allowed : 2.85 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.25), residues: 1020 helix: -0.22 (0.16), residues: 900 sheet: None (None), residues: 0 loop : -1.35 (0.57), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP I 439 PHE 0.013 0.002 PHE H 501 TYR 0.010 0.001 TYR H 474 ARG 0.008 0.001 ARG C 488 *********************** 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 468 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 465 time to evaluate : 1.009 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: A 461 ASP cc_start: 0.9172 (m-30) cc_final: 0.8794 (t70) REVERT: A 470 MET cc_start: 0.9134 (mtt) cc_final: 0.8719 (mtt) REVERT: A 471 LYS cc_start: 0.9110 (ptpp) cc_final: 0.8704 (ptmt) REVERT: A 480 LYS cc_start: 0.9456 (mmtm) cc_final: 0.9047 (mmmt) REVERT: A 486 LYS cc_start: 0.9497 (mttp) cc_final: 0.8901 (mttp) REVERT: A 489 GLN cc_start: 0.9293 (tp40) cc_final: 0.8581 (tp40) REVERT: A 492 ASP cc_start: 0.9357 (m-30) cc_final: 0.9137 (m-30) REVERT: A 500 GLU cc_start: 0.8383 (pm20) cc_final: 0.8091 (pm20) REVERT: B 471 LYS cc_start: 0.9372 (ptmm) cc_final: 0.8719 (ptmm) REVERT: B 492 ASP cc_start: 0.8957 (m-30) cc_final: 0.8570 (m-30) REVERT: B 513 LYS cc_start: 0.9216 (pptt) cc_final: 0.8675 (mmmt) REVERT: C 459 SER cc_start: 0.9817 (m) cc_final: 0.9489 (p) REVERT: C 461 ASP cc_start: 0.9261 (m-30) cc_final: 0.9008 (m-30) REVERT: C 470 MET cc_start: 0.8976 (mtm) cc_final: 0.7831 (mtt) REVERT: C 473 ASP cc_start: 0.9363 (m-30) cc_final: 0.9116 (m-30) REVERT: C 478 SER cc_start: 0.9597 (t) cc_final: 0.9355 (p) REVERT: C 489 GLN cc_start: 0.8480 (mp10) cc_final: 0.8170 (mp10) REVERT: C 491 LEU cc_start: 0.8905 (mp) cc_final: 0.8488 (tt) REVERT: C 492 ASP cc_start: 0.9307 (m-30) cc_final: 0.9007 (m-30) REVERT: C 495 ASP cc_start: 0.9264 (t70) cc_final: 0.8961 (t0) REVERT: C 513 LYS cc_start: 0.8878 (mmmt) cc_final: 0.8655 (tppt) REVERT: D 441 GLN cc_start: 0.8218 (tp40) cc_final: 0.8015 (tp-100) REVERT: D 452 THR cc_start: 0.8547 (p) cc_final: 0.7876 (t) REVERT: D 461 ASP cc_start: 0.9386 (m-30) cc_final: 0.9068 (t70) REVERT: D 469 ILE cc_start: 0.9276 (tt) cc_final: 0.8972 (tt) REVERT: D 472 GLU cc_start: 0.8316 (tt0) cc_final: 0.7799 (tt0) REVERT: D 474 TYR cc_start: 0.9406 (t80) cc_final: 0.9147 (t80) REVERT: D 476 LEU cc_start: 0.9157 (mt) cc_final: 0.8919 (mt) REVERT: D 478 SER cc_start: 0.9472 (t) cc_final: 0.9197 (p) REVERT: D 503 LYS cc_start: 0.9039 (pttm) cc_final: 0.8787 (pttm) REVERT: E 438 GLN cc_start: 0.9320 (OUTLIER) cc_final: 0.9096 (pp30) REVERT: E 445 GLU cc_start: 0.9024 (pm20) cc_final: 0.8715 (pm20) REVERT: E 446 ASP cc_start: 0.9178 (m-30) cc_final: 0.8846 (m-30) REVERT: E 453 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8190 (tp30) REVERT: E 461 ASP cc_start: 0.8847 (m-30) cc_final: 0.7474 (t70) REVERT: E 471 LYS cc_start: 0.8924 (tttt) cc_final: 0.8482 (tmtt) REVERT: E 473 ASP cc_start: 0.9016 (m-30) cc_final: 0.8405 (m-30) REVERT: E 474 TYR cc_start: 0.9207 (t80) cc_final: 0.8999 (t80) REVERT: E 476 LEU cc_start: 0.9174 (mt) cc_final: 0.8050 (mt) REVERT: E 480 LYS cc_start: 0.8670 (mtpt) cc_final: 0.7986 (mtpp) REVERT: E 483 ARG cc_start: 0.9012 (mtt180) cc_final: 0.8717 (ttm170) REVERT: E 486 LYS cc_start: 0.9346 (mtpp) cc_final: 0.9082 (mttm) REVERT: E 489 GLN cc_start: 0.8929 (mp10) cc_final: 0.8561 (mp10) REVERT: E 494 THR cc_start: 0.9567 (m) cc_final: 0.9199 (m) REVERT: E 501 PHE cc_start: 0.8832 (t80) cc_final: 0.7857 (t80) REVERT: F 446 ASP cc_start: 0.9053 (t0) cc_final: 0.8731 (t0) REVERT: F 480 LYS cc_start: 0.7642 (pttm) cc_final: 0.7436 (pttm) REVERT: G 461 ASP cc_start: 0.8998 (m-30) cc_final: 0.8257 (t0) REVERT: G 475 GLU cc_start: 0.7826 (mp0) cc_final: 0.7403 (tp30) REVERT: G 497 GLN cc_start: 0.7056 (mm-40) cc_final: 0.6791 (tp40) REVERT: G 500 GLU cc_start: 0.8173 (pt0) cc_final: 0.7362 (pm20) REVERT: H 470 MET cc_start: 0.9046 (mpp) cc_final: 0.7865 (mpp) REVERT: H 472 GLU cc_start: 0.8645 (tt0) cc_final: 0.8331 (tt0) REVERT: H 480 LYS cc_start: 0.8867 (ptmt) cc_final: 0.8532 (ptpp) REVERT: H 485 SER cc_start: 0.9417 (m) cc_final: 0.8992 (p) REVERT: H 486 LYS cc_start: 0.9407 (mtpt) cc_final: 0.9059 (mtpp) REVERT: H 489 GLN cc_start: 0.8542 (tt0) cc_final: 0.8101 (tt0) REVERT: H 500 GLU cc_start: 0.8226 (mp0) cc_final: 0.7787 (pm20) REVERT: H 501 PHE cc_start: 0.8917 (t80) cc_final: 0.8422 (t80) REVERT: H 507 GLN cc_start: 0.9062 (mp10) cc_final: 0.8679 (mp10) REVERT: H 515 MET cc_start: 0.3209 (mmp) cc_final: 0.2343 (tpp) REVERT: I 445 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8199 (mp0) REVERT: I 463 LEU cc_start: 0.9402 (mt) cc_final: 0.9190 (mt) REVERT: I 479 THR cc_start: 0.9104 (m) cc_final: 0.8851 (p) REVERT: J 445 GLU cc_start: 0.8801 (mp0) cc_final: 0.8564 (mp0) REVERT: J 449 ASN cc_start: 0.9314 (m-40) cc_final: 0.8970 (m-40) REVERT: J 451 MET cc_start: 0.8511 (tpp) cc_final: 0.8287 (tpp) REVERT: J 453 GLU cc_start: 0.8941 (tm-30) cc_final: 0.8664 (tm-30) REVERT: J 470 MET cc_start: 0.8278 (mtt) cc_final: 0.7762 (mtt) REVERT: J 494 THR cc_start: 0.9632 (m) cc_final: 0.9424 (m) REVERT: J 495 ASP cc_start: 0.9494 (m-30) cc_final: 0.9259 (m-30) REVERT: J 501 PHE cc_start: 0.9085 (t80) cc_final: 0.8350 (t80) REVERT: K 444 ARG cc_start: 0.7092 (ttm170) cc_final: 0.6638 (ptt180) REVERT: K 456 LEU cc_start: 0.9597 (tp) cc_final: 0.9386 (tp) REVERT: K 464 LEU cc_start: 0.9450 (tp) cc_final: 0.9249 (tt) REVERT: K 471 LYS cc_start: 0.9185 (mmmm) cc_final: 0.8476 (ttpt) REVERT: K 476 LEU cc_start: 0.9381 (mt) cc_final: 0.9028 (mt) REVERT: K 478 SER cc_start: 0.9210 (t) cc_final: 0.8918 (p) REVERT: K 480 LYS cc_start: 0.9401 (mmtt) cc_final: 0.8916 (mmmm) REVERT: L 437 GLN cc_start: 0.9462 (pt0) cc_final: 0.9076 (pm20) REVERT: L 441 GLN cc_start: 0.9248 (mt0) cc_final: 0.8828 (tm-30) REVERT: L 460 LEU cc_start: 0.9476 (mp) cc_final: 0.9180 (mp) REVERT: L 472 GLU cc_start: 0.8134 (tt0) cc_final: 0.7535 (tt0) REVERT: L 475 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8545 (mt-10) REVERT: L 480 LYS cc_start: 0.9566 (mmtm) cc_final: 0.9110 (mmmm) REVERT: L 489 GLN cc_start: 0.9347 (mm-40) cc_final: 0.9106 (mm-40) REVERT: L 500 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8730 (mm-30) REVERT: L 503 LYS cc_start: 0.9406 (mtpp) cc_final: 0.9096 (mtpp) outliers start: 3 outliers final: 0 residues processed: 466 average time/residue: 0.2301 time to fit residues: 138.5458 Evaluate side-chains 391 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 390 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 61 optimal weight: 0.0980 chunk 24 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 22 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 489 GLN C 437 GLN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 457 ASN D 458 GLN E 512 ASN F 438 GLN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 ASN G 514 GLN ** H 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 514 GLN I 458 GLN ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 458 GLN J 512 ASN K 449 ASN K 512 ASN L 489 GLN L 512 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.066021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.051757 restraints weight = 38052.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.053644 restraints weight = 25754.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.055093 restraints weight = 19307.934| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 1.9071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8328 Z= 0.263 Angle : 0.763 8.190 11184 Z= 0.410 Chirality : 0.044 0.176 1332 Planarity : 0.004 0.066 1440 Dihedral : 5.265 33.351 1092 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.21 % Allowed : 3.16 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.25), residues: 1020 helix: -0.20 (0.16), residues: 888 sheet: None (None), residues: 0 loop : -1.75 (0.52), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP C 439 PHE 0.015 0.003 PHE G 501 TYR 0.011 0.002 TYR G 474 ARG 0.009 0.001 ARG C 488 *********************** 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 468 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 466 time to evaluate : 1.117 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 461 ASP cc_start: 0.9126 (m-30) cc_final: 0.8692 (t70) REVERT: A 470 MET cc_start: 0.9032 (mtt) cc_final: 0.8702 (mtt) REVERT: A 489 GLN cc_start: 0.9434 (tp40) cc_final: 0.8798 (tp40) REVERT: A 492 ASP cc_start: 0.9350 (m-30) cc_final: 0.9149 (m-30) REVERT: A 496 ILE cc_start: 0.9324 (pt) cc_final: 0.9108 (pt) REVERT: A 500 GLU cc_start: 0.8620 (pm20) cc_final: 0.8019 (pm20) REVERT: A 513 LYS cc_start: 0.9212 (mmpt) cc_final: 0.9009 (mmmt) REVERT: B 480 LYS cc_start: 0.9188 (mtmt) cc_final: 0.8966 (ptpp) REVERT: B 486 LYS cc_start: 0.9433 (mttp) cc_final: 0.9181 (mmtm) REVERT: B 489 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8446 (mp10) REVERT: B 492 ASP cc_start: 0.8995 (m-30) cc_final: 0.8498 (m-30) REVERT: B 499 GLU cc_start: 0.8027 (mm-30) cc_final: 0.6830 (mm-30) REVERT: B 500 GLU cc_start: 0.8522 (pm20) cc_final: 0.8283 (pm20) REVERT: B 513 LYS cc_start: 0.9299 (pptt) cc_final: 0.8808 (mmmt) REVERT: C 440 ILE cc_start: 0.9276 (mt) cc_final: 0.8540 (mt) REVERT: C 444 ARG cc_start: 0.8480 (tpp-160) cc_final: 0.7810 (mmm-85) REVERT: C 456 LEU cc_start: 0.9585 (tp) cc_final: 0.9354 (tp) REVERT: C 459 SER cc_start: 0.9821 (m) cc_final: 0.9554 (p) REVERT: C 461 ASP cc_start: 0.9241 (m-30) cc_final: 0.8970 (m-30) REVERT: C 470 MET cc_start: 0.8399 (mtm) cc_final: 0.7862 (mtm) REVERT: C 473 ASP cc_start: 0.9370 (m-30) cc_final: 0.9073 (m-30) REVERT: C 478 SER cc_start: 0.9680 (t) cc_final: 0.9403 (p) REVERT: C 491 LEU cc_start: 0.9226 (mp) cc_final: 0.8997 (mt) REVERT: C 495 ASP cc_start: 0.9353 (t70) cc_final: 0.9081 (t0) REVERT: C 515 MET cc_start: 0.6899 (tpt) cc_final: 0.6432 (mmt) REVERT: D 441 GLN cc_start: 0.8726 (tp40) cc_final: 0.8076 (tp-100) REVERT: D 461 ASP cc_start: 0.9332 (m-30) cc_final: 0.8598 (t0) REVERT: D 470 MET cc_start: 0.8784 (ptt) cc_final: 0.8145 (ptt) REVERT: D 474 TYR cc_start: 0.9464 (t80) cc_final: 0.9177 (t80) REVERT: D 478 SER cc_start: 0.9568 (t) cc_final: 0.9263 (p) REVERT: E 443 LYS cc_start: 0.9389 (ptpt) cc_final: 0.8305 (ptpp) REVERT: E 446 ASP cc_start: 0.9309 (m-30) cc_final: 0.8796 (p0) REVERT: E 453 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8135 (tp30) REVERT: E 461 ASP cc_start: 0.8689 (m-30) cc_final: 0.7630 (t70) REVERT: E 471 LYS cc_start: 0.8953 (tttt) cc_final: 0.8552 (tmtt) REVERT: E 483 ARG cc_start: 0.9012 (mtt180) cc_final: 0.8676 (ttm170) REVERT: E 489 GLN cc_start: 0.8865 (mp10) cc_final: 0.8443 (mp10) REVERT: E 494 THR cc_start: 0.9658 (m) cc_final: 0.9312 (m) REVERT: E 501 PHE cc_start: 0.8909 (t80) cc_final: 0.7923 (t80) REVERT: E 507 GLN cc_start: 0.9417 (tp40) cc_final: 0.9132 (tp-100) REVERT: F 441 GLN cc_start: 0.8421 (tp-100) cc_final: 0.7978 (tp40) REVERT: F 446 ASP cc_start: 0.9010 (t0) cc_final: 0.8724 (t0) REVERT: F 461 ASP cc_start: 0.8962 (t0) cc_final: 0.8715 (t70) REVERT: G 445 GLU cc_start: 0.8541 (pm20) cc_final: 0.8259 (pm20) REVERT: G 446 ASP cc_start: 0.8689 (m-30) cc_final: 0.8486 (m-30) REVERT: G 461 ASP cc_start: 0.9178 (m-30) cc_final: 0.8130 (t70) REVERT: G 464 LEU cc_start: 0.9342 (mt) cc_final: 0.9082 (mt) REVERT: G 475 GLU cc_start: 0.7799 (mp0) cc_final: 0.7219 (tm-30) REVERT: G 500 GLU cc_start: 0.8227 (pt0) cc_final: 0.7603 (pm20) REVERT: G 501 PHE cc_start: 0.8707 (t80) cc_final: 0.8443 (t80) REVERT: H 470 MET cc_start: 0.9026 (mpp) cc_final: 0.8023 (mtt) REVERT: H 476 LEU cc_start: 0.9424 (mt) cc_final: 0.9158 (mt) REVERT: H 480 LYS cc_start: 0.8922 (ptmt) cc_final: 0.8551 (ptmt) REVERT: H 500 GLU cc_start: 0.8343 (mp0) cc_final: 0.7984 (pm20) REVERT: H 501 PHE cc_start: 0.9048 (t80) cc_final: 0.8502 (t80) REVERT: H 505 ILE cc_start: 0.9385 (mm) cc_final: 0.9111 (mm) REVERT: H 515 MET cc_start: 0.3664 (mmp) cc_final: 0.2906 (mmp) REVERT: I 445 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8296 (mp0) REVERT: I 461 ASP cc_start: 0.8793 (t70) cc_final: 0.8249 (t70) REVERT: I 488 ARG cc_start: 0.8609 (ptp-110) cc_final: 0.8112 (ptp-110) REVERT: J 438 GLN cc_start: 0.9105 (pt0) cc_final: 0.8748 (pp30) REVERT: J 445 GLU cc_start: 0.8794 (mp0) cc_final: 0.8398 (mp0) REVERT: J 449 ASN cc_start: 0.9296 (m-40) cc_final: 0.8969 (m-40) REVERT: J 451 MET cc_start: 0.8621 (tpp) cc_final: 0.8414 (tpp) REVERT: J 453 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8616 (tm-30) REVERT: J 470 MET cc_start: 0.8261 (mtt) cc_final: 0.7673 (mtt) REVERT: J 495 ASP cc_start: 0.9480 (m-30) cc_final: 0.9230 (m-30) REVERT: J 501 PHE cc_start: 0.9011 (t80) cc_final: 0.8363 (t80) REVERT: K 444 ARG cc_start: 0.7219 (ttm170) cc_final: 0.6845 (ptt-90) REVERT: K 449 ASN cc_start: 0.9403 (m-40) cc_final: 0.8929 (p0) REVERT: K 464 LEU cc_start: 0.9569 (tp) cc_final: 0.9332 (tt) REVERT: K 470 MET cc_start: 0.7271 (mtt) cc_final: 0.6763 (mtt) REVERT: K 471 LYS cc_start: 0.9352 (mmmm) cc_final: 0.8909 (tttm) REVERT: K 476 LEU cc_start: 0.9486 (mt) cc_final: 0.9243 (mt) REVERT: K 478 SER cc_start: 0.9383 (t) cc_final: 0.9031 (p) REVERT: K 480 LYS cc_start: 0.9551 (mmtt) cc_final: 0.9147 (mmmm) REVERT: L 437 GLN cc_start: 0.9465 (pt0) cc_final: 0.9036 (pm20) REVERT: L 441 GLN cc_start: 0.9297 (mt0) cc_final: 0.8909 (tm-30) REVERT: L 445 GLU cc_start: 0.8867 (pm20) cc_final: 0.8522 (pm20) REVERT: L 446 ASP cc_start: 0.8958 (m-30) cc_final: 0.8672 (m-30) REVERT: L 460 LEU cc_start: 0.9529 (mp) cc_final: 0.9212 (mp) REVERT: L 472 GLU cc_start: 0.8112 (tt0) cc_final: 0.7531 (tt0) REVERT: L 475 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8474 (mt-10) REVERT: L 476 LEU cc_start: 0.9327 (mt) cc_final: 0.9104 (mt) REVERT: L 480 LYS cc_start: 0.9507 (mmtm) cc_final: 0.9290 (mmmm) REVERT: L 492 ASP cc_start: 0.9115 (m-30) cc_final: 0.8666 (m-30) REVERT: L 500 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8741 (mm-30) REVERT: L 503 LYS cc_start: 0.9391 (mtpp) cc_final: 0.9096 (mtpp) outliers start: 2 outliers final: 0 residues processed: 467 average time/residue: 0.2226 time to fit residues: 136.5042 Evaluate side-chains 399 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 398 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 51 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 64 optimal weight: 20.0000 chunk 93 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 3 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 450 GLN C 458 GLN D 441 GLN ** D 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN E 512 ASN F 438 GLN ** F 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 458 GLN ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 512 ASN K 458 GLN K 512 ASN ** L 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 512 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.064439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.050756 restraints weight = 38363.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.052632 restraints weight = 25533.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.054084 restraints weight = 19016.519| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 1.9747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8328 Z= 0.261 Angle : 0.772 8.892 11184 Z= 0.410 Chirality : 0.044 0.173 1332 Planarity : 0.004 0.067 1440 Dihedral : 5.329 33.750 1092 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.11 % Allowed : 1.90 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.25), residues: 1020 helix: -0.26 (0.16), residues: 888 sheet: None (None), residues: 0 loop : -1.78 (0.53), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP B 439 PHE 0.016 0.002 PHE G 501 TYR 0.011 0.002 TYR I 474 ARG 0.010 0.001 ARG C 488 *********************** 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 464 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 463 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 ASP cc_start: 0.9062 (m-30) cc_final: 0.8785 (t70) REVERT: A 470 MET cc_start: 0.9038 (mtt) cc_final: 0.8605 (mtt) REVERT: A 480 LYS cc_start: 0.9464 (mmmt) cc_final: 0.9201 (mmmt) REVERT: A 489 GLN cc_start: 0.9462 (tp40) cc_final: 0.8821 (tp40) REVERT: A 492 ASP cc_start: 0.9304 (m-30) cc_final: 0.9059 (m-30) REVERT: A 500 GLU cc_start: 0.8693 (pm20) cc_final: 0.7915 (pm20) REVERT: B 441 GLN cc_start: 0.8630 (mm110) cc_final: 0.8424 (mm110) REVERT: B 471 LYS cc_start: 0.9308 (ptmm) cc_final: 0.9028 (ptmm) REVERT: B 472 GLU cc_start: 0.8738 (pm20) cc_final: 0.8161 (pm20) REVERT: B 476 LEU cc_start: 0.9840 (tp) cc_final: 0.9582 (tp) REVERT: B 480 LYS cc_start: 0.9271 (mtmt) cc_final: 0.8846 (mttp) REVERT: B 486 LYS cc_start: 0.9439 (mttp) cc_final: 0.9168 (mmtm) REVERT: B 492 ASP cc_start: 0.8824 (m-30) cc_final: 0.8596 (m-30) REVERT: B 499 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7438 (mm-30) REVERT: B 513 LYS cc_start: 0.9241 (pptt) cc_final: 0.8786 (mmmt) REVERT: C 440 ILE cc_start: 0.9365 (mt) cc_final: 0.8472 (mt) REVERT: C 444 ARG cc_start: 0.8580 (tpp-160) cc_final: 0.7975 (mmm-85) REVERT: C 449 ASN cc_start: 0.8445 (m-40) cc_final: 0.8178 (m-40) REVERT: C 456 LEU cc_start: 0.9609 (tp) cc_final: 0.9399 (tp) REVERT: C 461 ASP cc_start: 0.9326 (m-30) cc_final: 0.9031 (m-30) REVERT: C 470 MET cc_start: 0.8426 (mtm) cc_final: 0.8013 (mtm) REVERT: C 473 ASP cc_start: 0.9289 (m-30) cc_final: 0.8984 (m-30) REVERT: C 478 SER cc_start: 0.9680 (t) cc_final: 0.9386 (p) REVERT: C 495 ASP cc_start: 0.9346 (t70) cc_final: 0.9104 (t0) REVERT: C 513 LYS cc_start: 0.8970 (mmpt) cc_final: 0.8698 (mmmt) REVERT: C 515 MET cc_start: 0.6851 (tpt) cc_final: 0.6394 (mmt) REVERT: D 441 GLN cc_start: 0.8741 (tp-100) cc_final: 0.8479 (tp-100) REVERT: D 461 ASP cc_start: 0.9085 (m-30) cc_final: 0.8613 (t0) REVERT: D 466 ARG cc_start: 0.8907 (mpp80) cc_final: 0.8665 (mtm-85) REVERT: D 478 SER cc_start: 0.9596 (t) cc_final: 0.9246 (p) REVERT: E 441 GLN cc_start: 0.8958 (mt0) cc_final: 0.8731 (mp10) REVERT: E 443 LYS cc_start: 0.9405 (ptpt) cc_final: 0.9082 (ptpp) REVERT: E 453 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8538 (tp30) REVERT: E 461 ASP cc_start: 0.8701 (m-30) cc_final: 0.7606 (t70) REVERT: E 471 LYS cc_start: 0.8824 (tttt) cc_final: 0.8527 (tmtt) REVERT: E 480 LYS cc_start: 0.8572 (mtpp) cc_final: 0.7978 (mtpp) REVERT: E 483 ARG cc_start: 0.9068 (mtt180) cc_final: 0.8848 (ttm170) REVERT: E 486 LYS cc_start: 0.9397 (mtpp) cc_final: 0.9115 (mttm) REVERT: E 489 GLN cc_start: 0.8736 (mp10) cc_final: 0.8458 (mp10) REVERT: E 495 ASP cc_start: 0.9414 (m-30) cc_final: 0.9149 (m-30) REVERT: E 501 PHE cc_start: 0.8877 (t80) cc_final: 0.8303 (t80) REVERT: E 507 GLN cc_start: 0.9436 (tp40) cc_final: 0.9159 (tp-100) REVERT: F 441 GLN cc_start: 0.8466 (tp-100) cc_final: 0.8118 (tp40) REVERT: F 446 ASP cc_start: 0.8871 (t0) cc_final: 0.8660 (t0) REVERT: F 460 LEU cc_start: 0.9307 (pp) cc_final: 0.9103 (pp) REVERT: G 445 GLU cc_start: 0.8493 (pm20) cc_final: 0.8230 (pm20) REVERT: G 446 ASP cc_start: 0.8634 (m-30) cc_final: 0.8369 (m-30) REVERT: G 461 ASP cc_start: 0.9310 (m-30) cc_final: 0.9028 (m-30) REVERT: G 464 LEU cc_start: 0.9546 (mt) cc_final: 0.9285 (mt) REVERT: G 475 GLU cc_start: 0.7726 (mp0) cc_final: 0.7396 (tm-30) REVERT: G 480 LYS cc_start: 0.9177 (tptt) cc_final: 0.8941 (ttmm) REVERT: G 489 GLN cc_start: 0.7970 (pm20) cc_final: 0.7638 (pm20) REVERT: G 515 MET cc_start: 0.2711 (mmp) cc_final: 0.2148 (mmp) REVERT: H 470 MET cc_start: 0.8748 (mpp) cc_final: 0.8166 (mtt) REVERT: H 472 GLU cc_start: 0.8673 (tt0) cc_final: 0.8181 (tt0) REVERT: H 473 ASP cc_start: 0.8865 (m-30) cc_final: 0.8635 (m-30) REVERT: H 476 LEU cc_start: 0.9389 (mt) cc_final: 0.9147 (mt) REVERT: H 500 GLU cc_start: 0.8418 (mp0) cc_final: 0.8051 (pm20) REVERT: H 501 PHE cc_start: 0.9126 (t80) cc_final: 0.8611 (t80) REVERT: H 505 ILE cc_start: 0.9378 (mm) cc_final: 0.9166 (mm) REVERT: I 453 GLU cc_start: 0.9267 (tm-30) cc_final: 0.8994 (tm-30) REVERT: I 461 ASP cc_start: 0.8831 (t70) cc_final: 0.8114 (t70) REVERT: I 463 LEU cc_start: 0.9483 (mt) cc_final: 0.9268 (mt) REVERT: I 469 ILE cc_start: 0.9419 (tt) cc_final: 0.9133 (tt) REVERT: I 480 LYS cc_start: 0.9196 (mttp) cc_final: 0.8846 (mttt) REVERT: I 495 ASP cc_start: 0.9340 (m-30) cc_final: 0.9043 (m-30) REVERT: I 499 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7537 (mm-30) REVERT: I 515 MET cc_start: 0.6192 (tpt) cc_final: 0.5411 (tpp) REVERT: J 438 GLN cc_start: 0.9103 (pt0) cc_final: 0.8742 (pp30) REVERT: J 445 GLU cc_start: 0.8840 (mp0) cc_final: 0.8376 (mp0) REVERT: J 449 ASN cc_start: 0.9293 (m-40) cc_final: 0.8936 (m-40) REVERT: J 451 MET cc_start: 0.8684 (tpp) cc_final: 0.8451 (tpp) REVERT: J 453 GLU cc_start: 0.9037 (tm-30) cc_final: 0.8698 (tm-30) REVERT: J 470 MET cc_start: 0.8525 (mtt) cc_final: 0.7916 (mtt) REVERT: J 495 ASP cc_start: 0.9476 (m-30) cc_final: 0.9239 (m-30) REVERT: J 501 PHE cc_start: 0.9093 (t80) cc_final: 0.8490 (t80) REVERT: K 444 ARG cc_start: 0.7309 (ttm170) cc_final: 0.6668 (ptt-90) REVERT: K 458 GLN cc_start: 0.9275 (OUTLIER) cc_final: 0.9025 (pp30) REVERT: K 464 LEU cc_start: 0.9633 (tp) cc_final: 0.9420 (mt) REVERT: K 469 ILE cc_start: 0.9368 (tt) cc_final: 0.8817 (mm) REVERT: K 471 LYS cc_start: 0.9395 (mmmm) cc_final: 0.8894 (ttpp) REVERT: K 478 SER cc_start: 0.9426 (t) cc_final: 0.9101 (p) REVERT: K 480 LYS cc_start: 0.9626 (mmtt) cc_final: 0.9300 (mtmt) REVERT: K 509 LEU cc_start: 0.9425 (mm) cc_final: 0.9210 (mm) REVERT: L 437 GLN cc_start: 0.9494 (pt0) cc_final: 0.9053 (pm20) REVERT: L 441 GLN cc_start: 0.9351 (mt0) cc_final: 0.9133 (tm-30) REVERT: L 460 LEU cc_start: 0.9515 (mp) cc_final: 0.9202 (mp) REVERT: L 472 GLU cc_start: 0.8115 (tt0) cc_final: 0.7551 (tt0) REVERT: L 475 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8590 (mt-10) REVERT: L 489 GLN cc_start: 0.9300 (mm-40) cc_final: 0.8994 (mp10) REVERT: L 500 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8649 (mm-30) REVERT: L 503 LYS cc_start: 0.9424 (mtpp) cc_final: 0.9090 (mtpp) outliers start: 1 outliers final: 0 residues processed: 464 average time/residue: 0.2198 time to fit residues: 133.3494 Evaluate side-chains 405 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 404 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 90 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 94 optimal weight: 0.3980 chunk 66 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 458 GLN D 438 GLN ** D 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 512 ASN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 ASN ** H 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 512 ASN I 438 GLN ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 512 ASN ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN L 489 GLN L 512 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.065246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.051587 restraints weight = 38609.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.053445 restraints weight = 26134.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.054861 restraints weight = 19667.138| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 2.0073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8328 Z= 0.246 Angle : 0.786 8.586 11184 Z= 0.416 Chirality : 0.044 0.184 1332 Planarity : 0.004 0.064 1440 Dihedral : 5.200 32.973 1092 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.25), residues: 1020 helix: -0.24 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -1.75 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 439 PHE 0.016 0.002 PHE G 501 TYR 0.011 0.002 TYR I 474 ARG 0.008 0.001 ARG F 466 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 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 467 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 467 time to evaluate : 1.121 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: A 446 ASP cc_start: 0.8973 (t70) cc_final: 0.8457 (t0) REVERT: A 453 GLU cc_start: 0.9250 (tm-30) cc_final: 0.8640 (tm-30) REVERT: A 461 ASP cc_start: 0.9006 (m-30) cc_final: 0.8499 (t70) REVERT: A 470 MET cc_start: 0.8949 (mtt) cc_final: 0.8488 (mtt) REVERT: A 471 LYS cc_start: 0.9557 (mptt) cc_final: 0.9270 (mmmt) REVERT: A 489 GLN cc_start: 0.9428 (tp40) cc_final: 0.8651 (tp40) REVERT: A 492 ASP cc_start: 0.9323 (m-30) cc_final: 0.9065 (m-30) REVERT: A 500 GLU cc_start: 0.8322 (pm20) cc_final: 0.7665 (pm20) REVERT: B 471 LYS cc_start: 0.9322 (ptmm) cc_final: 0.8953 (pttt) REVERT: B 472 GLU cc_start: 0.8605 (pm20) cc_final: 0.7845 (pm20) REVERT: B 476 LEU cc_start: 0.9793 (tp) cc_final: 0.9475 (tp) REVERT: B 477 VAL cc_start: 0.9413 (p) cc_final: 0.9059 (p) REVERT: B 486 LYS cc_start: 0.9443 (mttp) cc_final: 0.9051 (mmtt) REVERT: B 499 GLU cc_start: 0.8052 (mm-30) cc_final: 0.6921 (mm-30) REVERT: B 500 GLU cc_start: 0.8356 (pm20) cc_final: 0.8116 (pm20) REVERT: B 503 LYS cc_start: 0.9441 (pttp) cc_final: 0.9008 (ptpp) REVERT: B 513 LYS cc_start: 0.9253 (pptt) cc_final: 0.8815 (mmmt) REVERT: C 440 ILE cc_start: 0.9342 (mt) cc_final: 0.8824 (mt) REVERT: C 444 ARG cc_start: 0.8554 (tpp-160) cc_final: 0.8017 (mmm-85) REVERT: C 449 ASN cc_start: 0.8421 (m-40) cc_final: 0.8186 (m-40) REVERT: C 459 SER cc_start: 0.9825 (m) cc_final: 0.9556 (p) REVERT: C 461 ASP cc_start: 0.9251 (m-30) cc_final: 0.8962 (m-30) REVERT: C 470 MET cc_start: 0.8224 (mtm) cc_final: 0.7800 (mtm) REVERT: C 473 ASP cc_start: 0.9215 (m-30) cc_final: 0.8996 (m-30) REVERT: C 478 SER cc_start: 0.9706 (t) cc_final: 0.9442 (p) REVERT: C 489 GLN cc_start: 0.7863 (mp10) cc_final: 0.7316 (mp10) REVERT: D 441 GLN cc_start: 0.8707 (tp-100) cc_final: 0.8278 (tp-100) REVERT: D 461 ASP cc_start: 0.9086 (m-30) cc_final: 0.8520 (t70) REVERT: D 466 ARG cc_start: 0.8860 (mpp80) cc_final: 0.8604 (mtm-85) REVERT: D 471 LYS cc_start: 0.9169 (tmtt) cc_final: 0.8890 (tmtt) REVERT: D 472 GLU cc_start: 0.9085 (mp0) cc_final: 0.8881 (tt0) REVERT: D 478 SER cc_start: 0.9625 (t) cc_final: 0.9343 (p) REVERT: D 480 LYS cc_start: 0.9065 (mmmm) cc_final: 0.8821 (mmmm) REVERT: E 443 LYS cc_start: 0.9441 (ptpt) cc_final: 0.8312 (ptpp) REVERT: E 446 ASP cc_start: 0.9284 (m-30) cc_final: 0.8852 (p0) REVERT: E 453 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8435 (tp30) REVERT: E 461 ASP cc_start: 0.8768 (m-30) cc_final: 0.7640 (t70) REVERT: E 480 LYS cc_start: 0.8590 (mtpp) cc_final: 0.8094 (mtpp) REVERT: E 486 LYS cc_start: 0.9429 (mtpp) cc_final: 0.9150 (mtpp) REVERT: E 489 GLN cc_start: 0.8705 (mp10) cc_final: 0.8408 (mp10) REVERT: E 495 ASP cc_start: 0.9386 (m-30) cc_final: 0.9172 (m-30) REVERT: E 507 GLN cc_start: 0.9376 (tp40) cc_final: 0.9100 (tp-100) REVERT: F 441 GLN cc_start: 0.8510 (tp-100) cc_final: 0.8105 (tp40) REVERT: F 446 ASP cc_start: 0.8826 (t0) cc_final: 0.8605 (t0) REVERT: G 445 GLU cc_start: 0.8319 (pm20) cc_final: 0.8110 (pm20) REVERT: G 461 ASP cc_start: 0.9212 (m-30) cc_final: 0.8932 (m-30) REVERT: G 475 GLU cc_start: 0.7621 (mp0) cc_final: 0.7152 (tm-30) REVERT: G 480 LYS cc_start: 0.9157 (tptt) cc_final: 0.8955 (ttmm) REVERT: G 489 GLN cc_start: 0.7889 (pm20) cc_final: 0.7669 (pm20) REVERT: G 515 MET cc_start: 0.2397 (mmp) cc_final: 0.2134 (mmp) REVERT: H 470 MET cc_start: 0.8568 (mpp) cc_final: 0.7277 (mtm) REVERT: H 472 GLU cc_start: 0.8566 (tt0) cc_final: 0.8208 (tt0) REVERT: H 473 ASP cc_start: 0.8800 (m-30) cc_final: 0.8285 (m-30) REVERT: H 476 LEU cc_start: 0.9385 (mt) cc_final: 0.9020 (mt) REVERT: H 480 LYS cc_start: 0.8866 (ptmt) cc_final: 0.8417 (ptpt) REVERT: H 489 GLN cc_start: 0.8341 (tt0) cc_final: 0.8069 (pp30) REVERT: H 500 GLU cc_start: 0.8395 (mp0) cc_final: 0.8009 (pm20) REVERT: H 501 PHE cc_start: 0.9136 (t80) cc_final: 0.8582 (t80) REVERT: H 507 GLN cc_start: 0.8882 (mp10) cc_final: 0.8666 (mp10) REVERT: I 461 ASP cc_start: 0.8894 (t70) cc_final: 0.8273 (t70) REVERT: I 471 LYS cc_start: 0.9048 (mtpp) cc_final: 0.8626 (ttpp) REVERT: I 480 LYS cc_start: 0.9166 (mttp) cc_final: 0.8874 (mttt) REVERT: I 495 ASP cc_start: 0.9346 (m-30) cc_final: 0.9012 (m-30) REVERT: I 499 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7524 (mm-30) REVERT: J 445 GLU cc_start: 0.8761 (mp0) cc_final: 0.8340 (mp0) REVERT: J 449 ASN cc_start: 0.9350 (m-40) cc_final: 0.8950 (m-40) REVERT: J 451 MET cc_start: 0.8692 (tpp) cc_final: 0.8469 (tpp) REVERT: J 453 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8817 (tp30) REVERT: J 470 MET cc_start: 0.8511 (mtt) cc_final: 0.7986 (mtt) REVERT: J 495 ASP cc_start: 0.9421 (m-30) cc_final: 0.9209 (m-30) REVERT: J 501 PHE cc_start: 0.8864 (t80) cc_final: 0.8024 (t80) REVERT: K 471 LYS cc_start: 0.9377 (mmmm) cc_final: 0.8916 (ttpt) REVERT: K 478 SER cc_start: 0.9460 (t) cc_final: 0.9169 (p) REVERT: K 504 VAL cc_start: 0.9507 (t) cc_final: 0.9082 (m) REVERT: K 509 LEU cc_start: 0.9486 (mm) cc_final: 0.9281 (mm) REVERT: L 437 GLN cc_start: 0.9443 (pt0) cc_final: 0.9158 (pm20) REVERT: L 445 GLU cc_start: 0.9002 (pm20) cc_final: 0.8794 (pm20) REVERT: L 460 LEU cc_start: 0.9511 (mp) cc_final: 0.9237 (mp) REVERT: L 472 GLU cc_start: 0.8103 (tt0) cc_final: 0.7605 (tt0) REVERT: L 475 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8640 (mt-10) REVERT: L 489 GLN cc_start: 0.9283 (mm110) cc_final: 0.8981 (mp10) REVERT: L 500 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8706 (mm-30) outliers start: 0 outliers final: 0 residues processed: 467 average time/residue: 0.2077 time to fit residues: 128.4808 Evaluate side-chains 397 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 64 optimal weight: 20.0000 chunk 76 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 512 ASN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 ASN ** H 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 512 ASN I 438 GLN ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 512 ASN ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 441 GLN ** K 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN L 512 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.066292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.052321 restraints weight = 37729.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.054238 restraints weight = 25289.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.055702 restraints weight = 18934.891| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 2.0326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8328 Z= 0.247 Angle : 0.808 8.339 11184 Z= 0.425 Chirality : 0.044 0.181 1332 Planarity : 0.005 0.082 1440 Dihedral : 5.223 32.044 1092 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % 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 : 8.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.25), residues: 1020 helix: -0.26 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -1.72 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 439 PHE 0.029 0.002 PHE E 501 TYR 0.024 0.003 TYR H 474 ARG 0.006 0.001 ARG J 466 ********************** 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 462 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 462 time to evaluate : 1.042 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: A 450 GLN cc_start: 0.8518 (mt0) cc_final: 0.8255 (pt0) REVERT: A 461 ASP cc_start: 0.9081 (m-30) cc_final: 0.8278 (t70) REVERT: A 470 MET cc_start: 0.8959 (mtt) cc_final: 0.7317 (mtt) REVERT: A 472 GLU cc_start: 0.9033 (mp0) cc_final: 0.8651 (pm20) REVERT: A 473 ASP cc_start: 0.9074 (m-30) cc_final: 0.8662 (m-30) REVERT: A 480 LYS cc_start: 0.9481 (mmmt) cc_final: 0.9161 (mmmt) REVERT: A 486 LYS cc_start: 0.9584 (mttp) cc_final: 0.8870 (mtmm) REVERT: A 489 GLN cc_start: 0.9425 (tp40) cc_final: 0.8634 (tp40) REVERT: A 492 ASP cc_start: 0.9339 (m-30) cc_final: 0.9093 (m-30) REVERT: A 500 GLU cc_start: 0.8402 (pm20) cc_final: 0.7805 (pm20) REVERT: B 472 GLU cc_start: 0.8692 (pm20) cc_final: 0.8106 (pm20) REVERT: B 476 LEU cc_start: 0.9807 (tp) cc_final: 0.9603 (tp) REVERT: B 486 LYS cc_start: 0.9484 (mttp) cc_final: 0.9160 (mmtt) REVERT: B 499 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7123 (mm-30) REVERT: B 503 LYS cc_start: 0.9416 (pttp) cc_final: 0.9048 (ptpp) REVERT: B 513 LYS cc_start: 0.9229 (pptt) cc_final: 0.8753 (mmmt) REVERT: B 515 MET cc_start: 0.7665 (tmm) cc_final: 0.7405 (ppp) REVERT: C 440 ILE cc_start: 0.9303 (mt) cc_final: 0.8762 (mt) REVERT: C 444 ARG cc_start: 0.8514 (tpp-160) cc_final: 0.7860 (mmm-85) REVERT: C 449 ASN cc_start: 0.8448 (m-40) cc_final: 0.8203 (m-40) REVERT: C 459 SER cc_start: 0.9818 (m) cc_final: 0.9567 (p) REVERT: C 461 ASP cc_start: 0.9322 (m-30) cc_final: 0.9021 (m-30) REVERT: C 466 ARG cc_start: 0.9157 (mmm-85) cc_final: 0.8921 (mmm-85) REVERT: C 469 ILE cc_start: 0.9152 (tt) cc_final: 0.8901 (tt) REVERT: C 473 ASP cc_start: 0.9339 (m-30) cc_final: 0.8968 (m-30) REVERT: C 478 SER cc_start: 0.9712 (t) cc_final: 0.9398 (p) REVERT: C 480 LYS cc_start: 0.9125 (mttp) cc_final: 0.8839 (mttm) REVERT: C 486 LYS cc_start: 0.9075 (mtmm) cc_final: 0.8720 (mttp) REVERT: C 500 GLU cc_start: 0.7949 (pp20) cc_final: 0.7700 (tm-30) REVERT: C 515 MET cc_start: 0.6892 (tpt) cc_final: 0.6516 (mmt) REVERT: D 441 GLN cc_start: 0.8706 (tp-100) cc_final: 0.8262 (tp-100) REVERT: D 449 ASN cc_start: 0.8647 (m110) cc_final: 0.8441 (m110) REVERT: D 461 ASP cc_start: 0.9051 (m-30) cc_final: 0.8579 (t0) REVERT: D 466 ARG cc_start: 0.8827 (mpp80) cc_final: 0.8595 (mtm-85) REVERT: D 472 GLU cc_start: 0.9086 (mp0) cc_final: 0.8824 (tt0) REVERT: D 478 SER cc_start: 0.9667 (t) cc_final: 0.9414 (p) REVERT: D 480 LYS cc_start: 0.9056 (mmmm) cc_final: 0.8797 (mmmm) REVERT: E 446 ASP cc_start: 0.9289 (m-30) cc_final: 0.8867 (p0) REVERT: E 461 ASP cc_start: 0.8797 (m-30) cc_final: 0.7755 (t70) REVERT: E 466 ARG cc_start: 0.8879 (ptp90) cc_final: 0.8528 (ptp90) REVERT: E 472 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8757 (tp30) REVERT: E 476 LEU cc_start: 0.9324 (mt) cc_final: 0.9088 (mt) REVERT: E 480 LYS cc_start: 0.8562 (mtpp) cc_final: 0.7924 (mtpp) REVERT: E 489 GLN cc_start: 0.8690 (mp10) cc_final: 0.8408 (mp10) REVERT: E 495 ASP cc_start: 0.9395 (m-30) cc_final: 0.9165 (m-30) REVERT: E 507 GLN cc_start: 0.9407 (tp40) cc_final: 0.9132 (tp-100) REVERT: F 441 GLN cc_start: 0.8546 (tp-100) cc_final: 0.8141 (tp40) REVERT: F 459 SER cc_start: 0.9616 (m) cc_final: 0.9326 (p) REVERT: F 460 LEU cc_start: 0.9368 (pp) cc_final: 0.9142 (pp) REVERT: G 461 ASP cc_start: 0.9221 (m-30) cc_final: 0.8943 (m-30) REVERT: G 464 LEU cc_start: 0.9501 (mt) cc_final: 0.9291 (mt) REVERT: G 475 GLU cc_start: 0.7482 (mp0) cc_final: 0.6992 (tm-30) REVERT: G 480 LYS cc_start: 0.9144 (tptt) cc_final: 0.8936 (ttmm) REVERT: G 500 GLU cc_start: 0.8724 (mp0) cc_final: 0.8388 (mp0) REVERT: G 501 PHE cc_start: 0.9252 (t80) cc_final: 0.8888 (t80) REVERT: G 515 MET cc_start: 0.2545 (mmp) cc_final: 0.2304 (mmp) REVERT: H 470 MET cc_start: 0.8611 (mpp) cc_final: 0.7315 (mtm) REVERT: H 472 GLU cc_start: 0.8618 (tt0) cc_final: 0.8329 (tt0) REVERT: H 473 ASP cc_start: 0.8848 (m-30) cc_final: 0.8524 (m-30) REVERT: H 476 LEU cc_start: 0.9412 (mt) cc_final: 0.9110 (mt) REVERT: H 480 LYS cc_start: 0.8838 (ptmt) cc_final: 0.8387 (ptpp) REVERT: H 488 ARG cc_start: 0.7725 (mmt90) cc_final: 0.7374 (mmt90) REVERT: H 489 GLN cc_start: 0.8317 (tt0) cc_final: 0.7889 (pt0) REVERT: H 500 GLU cc_start: 0.8474 (mp0) cc_final: 0.8047 (pm20) REVERT: H 501 PHE cc_start: 0.9040 (t80) cc_final: 0.8503 (t80) REVERT: I 461 ASP cc_start: 0.8903 (t70) cc_final: 0.8307 (t70) REVERT: I 471 LYS cc_start: 0.8976 (mtpp) cc_final: 0.8668 (ttpp) REVERT: I 480 LYS cc_start: 0.9111 (mttp) cc_final: 0.8687 (mttt) REVERT: I 495 ASP cc_start: 0.9380 (m-30) cc_final: 0.9133 (m-30) REVERT: I 499 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8107 (mm-30) REVERT: I 515 MET cc_start: 0.6358 (tpt) cc_final: 0.5593 (tpp) REVERT: J 445 GLU cc_start: 0.8744 (mp0) cc_final: 0.8377 (mp0) REVERT: J 449 ASN cc_start: 0.9336 (m-40) cc_final: 0.8977 (m-40) REVERT: J 453 GLU cc_start: 0.9129 (tm-30) cc_final: 0.8916 (tp30) REVERT: J 470 MET cc_start: 0.8604 (mtt) cc_final: 0.8401 (mtt) REVERT: J 491 LEU cc_start: 0.9693 (mm) cc_final: 0.9462 (mp) REVERT: J 495 ASP cc_start: 0.9424 (m-30) cc_final: 0.9198 (m-30) REVERT: J 501 PHE cc_start: 0.8866 (t80) cc_final: 0.8093 (t80) REVERT: K 469 ILE cc_start: 0.9317 (mm) cc_final: 0.9117 (mm) REVERT: K 471 LYS cc_start: 0.9440 (mmmm) cc_final: 0.8983 (ttpt) REVERT: K 478 SER cc_start: 0.9465 (t) cc_final: 0.9150 (p) REVERT: K 504 VAL cc_start: 0.9028 (t) cc_final: 0.8657 (m) REVERT: K 509 LEU cc_start: 0.9466 (mm) cc_final: 0.9239 (mm) REVERT: L 437 GLN cc_start: 0.9427 (pt0) cc_final: 0.9098 (pm20) REVERT: L 460 LEU cc_start: 0.9567 (mp) cc_final: 0.9284 (mp) REVERT: L 475 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8688 (mt-10) REVERT: L 476 LEU cc_start: 0.9346 (mt) cc_final: 0.9088 (mt) REVERT: L 480 LYS cc_start: 0.9538 (mmtm) cc_final: 0.9075 (mmmm) REVERT: L 492 ASP cc_start: 0.9141 (m-30) cc_final: 0.8936 (m-30) REVERT: L 500 GLU cc_start: 0.9327 (mm-30) cc_final: 0.8833 (mm-30) REVERT: L 503 LYS cc_start: 0.9526 (mtpp) cc_final: 0.9202 (mtpp) outliers start: 0 outliers final: 0 residues processed: 462 average time/residue: 0.2207 time to fit residues: 135.4880 Evaluate side-chains 399 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 69 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 80 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN E 512 ASN F 438 GLN F 449 ASN ** F 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 ASN ** H 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 512 ASN ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 512 ASN ** K 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN ** L 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 512 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.062742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.049620 restraints weight = 39036.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.051489 restraints weight = 25845.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.052810 restraints weight = 19041.579| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 2.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8328 Z= 0.303 Angle : 0.830 7.391 11184 Z= 0.446 Chirality : 0.047 0.179 1332 Planarity : 0.005 0.073 1440 Dihedral : 5.295 32.471 1092 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.25), residues: 1020 helix: -0.32 (0.17), residues: 888 sheet: None (None), residues: 0 loop : -1.73 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP C 439 PHE 0.031 0.003 PHE E 501 TYR 0.017 0.002 TYR G 474 ARG 0.013 0.001 ARG E 483 =============================================================================== Job complete usr+sys time: 3094.02 seconds wall clock time: 54 minutes 39.44 seconds (3279.44 seconds total)