Starting phenix.real_space_refine on Wed Feb 12 14:19:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5yrn_6842/02_2025/5yrn_6842.cif Found real_map, /net/cci-nas-00/data/ceres_data/5yrn_6842/02_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_6842/02_2025/5yrn_6842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5yrn_6842/02_2025/5yrn_6842.map" model { file = "/net/cci-nas-00/data/ceres_data/5yrn_6842/02_2025/5yrn_6842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5yrn_6842/02_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-5592/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: 2.79, per 1000 atoms: 0.34 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: 1.74 Conformation dependent library (CDL) restraints added in 1.3 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: 0.81 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: 2.14 Time building geometry restraints manager: 2.05 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: 0.07 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.990 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.500 ------------------------------------------------------------------------------- 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 : 0.953 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: 0.3100 time to fit residues: 158.5762 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 : 1.101 ------------------------------------------------------------------------------- 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 = 24)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.069884 restraints weight = 32968.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.072158 restraints weight = 22791.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.073895 restraints weight = 17204.086| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- 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 : 1.000 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: 0.7466 (mt) cc_final: 0.7181 (mt) REVERT: B 503 LYS cc_start: 0.9176 (ttmt) cc_final: 0.8850 (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: 0.8375 (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: 0.8881 (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: 0.7779 (mm-40) cc_final: 0.7565 (mt0) REVERT: G 440 ILE cc_start: 0.9081 (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: 0.7982 (tttt) cc_final: 0.7701 (pttt) REVERT: H 477 VAL cc_start: 0.7045 (t) cc_final: 0.5446 (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: 0.7445 (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: 0.8415 (tm-30) cc_final: 0.7815 (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: 0.2697 time to fit residues: 117.9017 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 : 1.062 ------------------------------------------------------------------------------- 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: 10.0000 chunk 91 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 44 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 88 optimal weight: 20.0000 chunk 94 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3603 r_free = 0.3603 target = 0.082402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.067133 restraints weight = 33281.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.069398 restraints weight = 23018.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.071163 restraints weight = 17226.809| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 1.0740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8328 Z= 0.229 Angle : 0.680 7.544 11184 Z= 0.368 Chirality : 0.043 0.388 1332 Planarity : 0.005 0.054 1440 Dihedral : 5.138 22.050 1092 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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: -1.18 (0.24), residues: 1020 helix: -0.56 (0.15), residues: 924 sheet: None (None), residues: 0 loop : -1.13 (0.58), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 439 PHE 0.012 0.003 PHE E 501 TYR 0.010 0.002 TYR J 474 ARG 0.009 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 387 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 1.000 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 443 LYS cc_start: 0.7778 (ptmm) cc_final: 0.7329 (ptmt) REVERT: A 448 VAL cc_start: 0.8707 (t) cc_final: 0.8497 (p) REVERT: A 456 LEU cc_start: 0.9602 (tp) cc_final: 0.9361 (tp) REVERT: A 461 ASP cc_start: 0.9041 (m-30) cc_final: 0.8733 (m-30) REVERT: A 471 LYS cc_start: 0.9054 (ptpp) cc_final: 0.8837 (ptmm) REVERT: A 484 THR cc_start: 0.9404 (p) cc_final: 0.9151 (p) REVERT: A 492 ASP cc_start: 0.8996 (m-30) cc_final: 0.8778 (m-30) REVERT: B 470 MET cc_start: 0.8167 (mtm) cc_final: 0.7802 (mtt) REVERT: B 503 LYS cc_start: 0.9147 (ttmt) cc_final: 0.8882 (tptt) REVERT: C 447 ILE cc_start: 0.7361 (mt) cc_final: 0.7076 (mt) REVERT: C 461 ASP cc_start: 0.8030 (m-30) cc_final: 0.7405 (m-30) REVERT: C 470 MET cc_start: 0.8477 (mtp) cc_final: 0.8193 (mtm) REVERT: D 450 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7432 (mt0) REVERT: D 480 LYS cc_start: 0.8852 (mttp) cc_final: 0.8504 (ttmm) REVERT: D 483 ARG cc_start: 0.8019 (mtt180) cc_final: 0.7212 (mtp-110) REVERT: D 507 GLN cc_start: 0.9088 (tm-30) cc_final: 0.8651 (tp-100) REVERT: D 513 LYS cc_start: 0.8637 (pptt) cc_final: 0.8382 (mmmt) REVERT: E 461 ASP cc_start: 0.9103 (m-30) cc_final: 0.8273 (t70) REVERT: E 473 ASP cc_start: 0.7964 (m-30) cc_final: 0.7502 (m-30) REVERT: E 480 LYS cc_start: 0.9071 (mtpt) cc_final: 0.8849 (ttmm) REVERT: E 483 ARG cc_start: 0.7875 (mtt180) cc_final: 0.7333 (ttm-80) REVERT: E 494 THR cc_start: 0.8915 (m) cc_final: 0.8685 (m) REVERT: E 503 LYS cc_start: 0.9476 (pttm) cc_final: 0.9188 (pttm) REVERT: F 515 MET cc_start: 0.7343 (tpt) cc_final: 0.7112 (tpt) REVERT: G 475 GLU cc_start: 0.7628 (mp0) cc_final: 0.6785 (pt0) REVERT: G 503 LYS cc_start: 0.9295 (pttm) cc_final: 0.8957 (pttp) REVERT: H 438 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8460 (pp30) REVERT: H 453 GLU cc_start: 0.8905 (pm20) cc_final: 0.8639 (pm20) REVERT: H 456 LEU cc_start: 0.9145 (tp) cc_final: 0.8918 (tp) REVERT: H 470 MET cc_start: 0.7399 (mpp) cc_final: 0.5875 (mpp) REVERT: H 473 ASP cc_start: 0.7038 (m-30) cc_final: 0.6275 (m-30) REVERT: H 477 VAL cc_start: 0.7282 (t) cc_final: 0.6842 (p) REVERT: H 486 LYS cc_start: 0.8407 (mtpt) cc_final: 0.8157 (mtpt) REVERT: I 482 THR cc_start: 0.8637 (p) cc_final: 0.7776 (p) REVERT: I 483 ARG cc_start: 0.7996 (mmp80) cc_final: 0.7490 (mtp-110) REVERT: I 515 MET cc_start: 0.6132 (tpp) cc_final: 0.5582 (tpp) REVERT: J 435 ILE cc_start: 0.7810 (mt) cc_final: 0.7594 (mt) REVERT: J 445 GLU cc_start: 0.7640 (mp0) cc_final: 0.6809 (mp0) REVERT: J 449 ASN cc_start: 0.8969 (m-40) cc_final: 0.8596 (m-40) REVERT: J 470 MET cc_start: 0.7301 (mtm) cc_final: 0.6882 (mtm) REVERT: J 486 LYS cc_start: 0.9122 (mtpt) cc_final: 0.8817 (mtpt) REVERT: J 499 GLU cc_start: 0.8238 (pp20) cc_final: 0.7951 (tm-30) REVERT: J 501 PHE cc_start: 0.8500 (t80) cc_final: 0.7956 (t80) REVERT: J 503 LYS cc_start: 0.8553 (pptt) cc_final: 0.8331 (pttm) REVERT: K 444 ARG cc_start: 0.5786 (ttm170) cc_final: 0.5224 (ptt180) REVERT: K 480 LYS cc_start: 0.6991 (mmtt) cc_final: 0.6676 (mmtt) REVERT: L 441 GLN cc_start: 0.9088 (mt0) cc_final: 0.8607 (tm-30) REVERT: L 453 GLU cc_start: 0.8425 (tm-30) cc_final: 0.7623 (tm-30) REVERT: L 457 ASN cc_start: 0.8493 (p0) cc_final: 0.7784 (p0) REVERT: L 489 GLN cc_start: 0.9086 (mm110) cc_final: 0.8627 (tt0) REVERT: L 496 ILE cc_start: 0.8364 (pt) cc_final: 0.7626 (mp) REVERT: L 509 LEU cc_start: 0.9241 (tt) cc_final: 0.9004 (pp) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.2628 time to fit residues: 129.2444 Evaluate side-chains 295 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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: 5.9990 chunk 28 optimal weight: 7.9990 chunk 64 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 449 ASN C 458 GLN ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 512 ASN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 ASN ** H 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN L 497 GLN L 512 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.076051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.062349 restraints weight = 34852.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.064577 restraints weight = 23120.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.066265 restraints weight = 16793.542| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 1.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 8328 Z= 0.285 Angle : 0.765 7.957 11184 Z= 0.406 Chirality : 0.044 0.183 1332 Planarity : 0.005 0.079 1440 Dihedral : 5.466 26.302 1092 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % 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: -0.75 (0.25), residues: 1020 helix: -0.25 (0.16), residues: 888 sheet: None (None), residues: 0 loop : -1.14 (0.50), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP K 439 PHE 0.019 0.003 PHE D 501 TYR 0.016 0.002 TYR B 474 ARG 0.005 0.001 ARG D 444 *********************** 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 444 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 444 time to evaluate : 1.063 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 466 ARG cc_start: 0.8783 (mmm160) cc_final: 0.8558 (mmm-85) REVERT: A 468 LEU cc_start: 0.9318 (mp) cc_final: 0.9040 (mm) REVERT: A 470 MET cc_start: 0.8857 (mtt) cc_final: 0.8388 (mtt) REVERT: A 471 LYS cc_start: 0.9102 (ptpp) cc_final: 0.8872 (ptmm) REVERT: A 476 LEU cc_start: 0.9538 (mt) cc_final: 0.9248 (mt) REVERT: A 480 LYS cc_start: 0.9567 (mmtt) cc_final: 0.9124 (mmmt) REVERT: A 489 GLN cc_start: 0.8272 (tm-30) cc_final: 0.8058 (tm-30) REVERT: A 513 LYS cc_start: 0.9087 (mmpt) cc_final: 0.8852 (mmmt) REVERT: B 448 VAL cc_start: 0.6617 (t) cc_final: 0.6390 (t) REVERT: B 460 LEU cc_start: 0.9340 (mt) cc_final: 0.9121 (mt) REVERT: B 468 LEU cc_start: 0.9327 (mt) cc_final: 0.8734 (tp) REVERT: B 470 MET cc_start: 0.8577 (mtm) cc_final: 0.7760 (mtt) REVERT: B 500 GLU cc_start: 0.8535 (tt0) cc_final: 0.8079 (pm20) REVERT: B 515 MET cc_start: 0.7361 (tmm) cc_final: 0.6953 (tmm) REVERT: C 440 ILE cc_start: 0.8874 (mt) cc_final: 0.8636 (mt) REVERT: C 456 LEU cc_start: 0.9334 (tp) cc_final: 0.9107 (tp) REVERT: C 461 ASP cc_start: 0.8651 (m-30) cc_final: 0.8358 (m-30) REVERT: C 471 LYS cc_start: 0.9136 (tmtt) cc_final: 0.7726 (tmtt) REVERT: C 488 ARG cc_start: 0.8353 (ptp-110) cc_final: 0.7432 (mmm160) REVERT: D 441 GLN cc_start: 0.8004 (tp-100) cc_final: 0.7722 (tp40) REVERT: D 471 LYS cc_start: 0.9350 (tptp) cc_final: 0.9071 (tmtt) REVERT: D 483 ARG cc_start: 0.8568 (mtt180) cc_final: 0.7809 (ttp80) REVERT: D 503 LYS cc_start: 0.9099 (pttm) cc_final: 0.8859 (pttm) REVERT: D 507 GLN cc_start: 0.9326 (tm-30) cc_final: 0.8867 (tp-100) REVERT: E 438 GLN cc_start: 0.9373 (pp30) cc_final: 0.9077 (pp30) REVERT: E 446 ASP cc_start: 0.9221 (m-30) cc_final: 0.9001 (m-30) REVERT: E 461 ASP cc_start: 0.8543 (m-30) cc_final: 0.7674 (t70) REVERT: E 471 LYS cc_start: 0.8859 (tttt) cc_final: 0.8114 (tmtt) REVERT: E 473 ASP cc_start: 0.8181 (m-30) cc_final: 0.7899 (m-30) REVERT: E 474 TYR cc_start: 0.9274 (t80) cc_final: 0.8967 (t80) REVERT: E 480 LYS cc_start: 0.9068 (mtpt) cc_final: 0.8642 (ttmm) REVERT: E 483 ARG cc_start: 0.8608 (mtt180) cc_final: 0.8190 (ttm170) REVERT: E 489 GLN cc_start: 0.8763 (mp10) cc_final: 0.8518 (mp10) REVERT: F 449 ASN cc_start: 0.7881 (m-40) cc_final: 0.7673 (m-40) REVERT: F 450 GLN cc_start: 0.8361 (mm110) cc_final: 0.7974 (mm-40) REVERT: F 458 GLN cc_start: 0.9477 (mm110) cc_final: 0.8648 (pt0) REVERT: F 461 ASP cc_start: 0.8819 (t70) cc_final: 0.7768 (t70) REVERT: G 446 ASP cc_start: 0.8408 (m-30) cc_final: 0.8188 (m-30) REVERT: G 461 ASP cc_start: 0.8498 (m-30) cc_final: 0.8224 (m-30) REVERT: G 475 GLU cc_start: 0.7843 (mp0) cc_final: 0.7061 (tm-30) REVERT: G 489 GLN cc_start: 0.8426 (mp10) cc_final: 0.7912 (mp10) REVERT: H 443 LYS cc_start: 0.9028 (mttt) cc_final: 0.8522 (mtmm) REVERT: H 451 MET cc_start: 0.9035 (tpt) cc_final: 0.8426 (tpp) REVERT: H 470 MET cc_start: 0.8421 (mpp) cc_final: 0.6661 (mpp) REVERT: H 473 ASP cc_start: 0.7874 (m-30) cc_final: 0.6971 (m-30) REVERT: I 447 ILE cc_start: 0.8352 (mt) cc_final: 0.8104 (mm) REVERT: I 461 ASP cc_start: 0.8366 (t70) cc_final: 0.7564 (t70) REVERT: I 476 LEU cc_start: 0.9184 (mt) cc_final: 0.8853 (mt) REVERT: I 482 THR cc_start: 0.9152 (p) cc_final: 0.7988 (p) REVERT: I 515 MET cc_start: 0.7061 (tpp) cc_final: 0.6527 (tpp) REVERT: J 445 GLU cc_start: 0.8448 (mp0) cc_final: 0.7706 (mp0) REVERT: J 448 VAL cc_start: 0.9265 (t) cc_final: 0.8972 (m) REVERT: J 449 ASN cc_start: 0.9355 (m-40) cc_final: 0.8713 (m-40) REVERT: J 458 GLN cc_start: 0.9472 (tp40) cc_final: 0.9236 (tm-30) REVERT: J 474 TYR cc_start: 0.9362 (t80) cc_final: 0.9098 (t80) REVERT: J 476 LEU cc_start: 0.9567 (mt) cc_final: 0.9321 (mt) REVERT: J 482 THR cc_start: 0.9109 (p) cc_final: 0.8577 (t) REVERT: J 484 THR cc_start: 0.8484 (p) cc_final: 0.8258 (p) REVERT: J 492 ASP cc_start: 0.9250 (m-30) cc_final: 0.9014 (m-30) REVERT: J 499 GLU cc_start: 0.8384 (pp20) cc_final: 0.7650 (tp30) REVERT: J 501 PHE cc_start: 0.8905 (t80) cc_final: 0.8520 (t80) REVERT: K 444 ARG cc_start: 0.6821 (ttm170) cc_final: 0.6150 (ptt-90) REVERT: K 453 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8276 (tm-30) REVERT: K 456 LEU cc_start: 0.8488 (tp) cc_final: 0.8286 (tp) REVERT: K 486 LYS cc_start: 0.8069 (mtpt) cc_final: 0.7844 (mttm) REVERT: L 441 GLN cc_start: 0.9090 (mt0) cc_final: 0.8516 (pp30) REVERT: L 469 ILE cc_start: 0.9301 (tt) cc_final: 0.9097 (tt) REVERT: L 486 LYS cc_start: 0.9326 (ttmm) cc_final: 0.9122 (mtmm) outliers start: 0 outliers final: 0 residues processed: 444 average time/residue: 0.2540 time to fit residues: 144.0848 Evaluate side-chains 340 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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: 0.7980 chunk 64 optimal weight: 30.0000 chunk 63 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 8 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 457 ASN E 437 GLN E 458 GLN E 512 ASN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 497 GLN H 450 GLN ** H 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 450 GLN K 449 ASN K 512 ASN L 450 GLN L 489 GLN L 497 GLN L 512 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.073666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.059225 restraints weight = 36324.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.061280 restraints weight = 24895.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.062869 restraints weight = 18705.546| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 1.5751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8328 Z= 0.238 Angle : 0.685 6.901 11184 Z= 0.369 Chirality : 0.042 0.233 1332 Planarity : 0.005 0.065 1440 Dihedral : 5.087 19.641 1092 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.46 (0.25), residues: 1020 helix: -0.00 (0.16), residues: 888 sheet: None (None), residues: 0 loop : -1.45 (0.49), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 439 PHE 0.011 0.002 PHE E 501 TYR 0.017 0.002 TYR H 474 ARG 0.008 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 452 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 452 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 ASP cc_start: 0.8302 (t0) cc_final: 0.8043 (t0) REVERT: A 461 ASP cc_start: 0.8980 (m-30) cc_final: 0.8582 (m-30) REVERT: A 471 LYS cc_start: 0.9093 (ptpp) cc_final: 0.8590 (ptmm) REVERT: A 476 LEU cc_start: 0.9667 (mt) cc_final: 0.9321 (mt) REVERT: A 479 THR cc_start: 0.8810 (t) cc_final: 0.8490 (p) REVERT: A 480 LYS cc_start: 0.9515 (mmtt) cc_final: 0.9191 (mmmt) REVERT: A 489 GLN cc_start: 0.8357 (tm-30) cc_final: 0.8117 (tm-30) REVERT: A 500 GLU cc_start: 0.8631 (pm20) cc_final: 0.8055 (pm20) REVERT: A 513 LYS cc_start: 0.9138 (mmpt) cc_final: 0.8920 (mmmt) REVERT: B 480 LYS cc_start: 0.8855 (mmmm) cc_final: 0.8359 (mmmm) REVERT: B 486 LYS cc_start: 0.9112 (mttp) cc_final: 0.8804 (mmtt) REVERT: B 495 ASP cc_start: 0.8040 (t70) cc_final: 0.7594 (t0) REVERT: B 503 LYS cc_start: 0.9266 (ptpp) cc_final: 0.9022 (pttp) REVERT: C 456 LEU cc_start: 0.9446 (tp) cc_final: 0.9207 (tp) REVERT: C 459 SER cc_start: 0.9738 (m) cc_final: 0.9447 (p) REVERT: C 470 MET cc_start: 0.8476 (mtp) cc_final: 0.8018 (mtm) REVERT: C 477 VAL cc_start: 0.9337 (t) cc_final: 0.9113 (t) REVERT: C 488 ARG cc_start: 0.8510 (ptp-110) cc_final: 0.7363 (mmm160) REVERT: C 491 LEU cc_start: 0.8536 (mp) cc_final: 0.7674 (mp) REVERT: C 492 ASP cc_start: 0.8986 (m-30) cc_final: 0.8758 (m-30) REVERT: C 513 LYS cc_start: 0.8758 (mmmt) cc_final: 0.8344 (mmmt) REVERT: C 515 MET cc_start: 0.7335 (tpt) cc_final: 0.7089 (mmt) REVERT: D 458 GLN cc_start: 0.8937 (mp10) cc_final: 0.8607 (pt0) REVERT: D 470 MET cc_start: 0.8719 (ptp) cc_final: 0.8450 (ptt) REVERT: D 474 TYR cc_start: 0.9176 (t80) cc_final: 0.8854 (t80) REVERT: D 477 VAL cc_start: 0.8764 (t) cc_final: 0.8439 (t) REVERT: D 478 SER cc_start: 0.9313 (t) cc_final: 0.9063 (p) REVERT: D 480 LYS cc_start: 0.9062 (mmtp) cc_final: 0.8732 (mmmm) REVERT: D 483 ARG cc_start: 0.8697 (mtt180) cc_final: 0.8193 (ttp80) REVERT: D 503 LYS cc_start: 0.9095 (pttm) cc_final: 0.8889 (pttm) REVERT: D 507 GLN cc_start: 0.9221 (tm-30) cc_final: 0.8843 (tp-100) REVERT: E 443 LYS cc_start: 0.9352 (ptpt) cc_final: 0.8903 (ptpp) REVERT: E 445 GLU cc_start: 0.8956 (pm20) cc_final: 0.8673 (pm20) REVERT: E 446 ASP cc_start: 0.9295 (m-30) cc_final: 0.8822 (m-30) REVERT: E 453 GLU cc_start: 0.8761 (tm-30) cc_final: 0.7688 (tp30) REVERT: E 461 ASP cc_start: 0.8356 (m-30) cc_final: 0.7317 (t70) REVERT: E 471 LYS cc_start: 0.8790 (tttt) cc_final: 0.8140 (tmtt) REVERT: E 473 ASP cc_start: 0.8822 (m-30) cc_final: 0.8618 (m-30) REVERT: E 486 LYS cc_start: 0.9101 (mtpp) cc_final: 0.8618 (mtpp) REVERT: E 489 GLN cc_start: 0.8815 (mp10) cc_final: 0.8576 (mp10) REVERT: F 449 ASN cc_start: 0.8281 (m-40) cc_final: 0.7851 (m-40) REVERT: F 461 ASP cc_start: 0.8083 (t70) cc_final: 0.6942 (t0) REVERT: G 446 ASP cc_start: 0.8680 (m-30) cc_final: 0.7959 (m-30) REVERT: G 467 ASP cc_start: 0.8413 (t70) cc_final: 0.8143 (t70) REVERT: G 475 GLU cc_start: 0.7826 (mp0) cc_final: 0.7181 (tp30) REVERT: G 489 GLN cc_start: 0.8475 (mp10) cc_final: 0.8266 (mp10) REVERT: G 503 LYS cc_start: 0.9413 (ptpp) cc_final: 0.8890 (pttp) REVERT: H 470 MET cc_start: 0.8767 (mpp) cc_final: 0.7004 (mpp) REVERT: H 473 ASP cc_start: 0.8522 (m-30) cc_final: 0.7624 (m-30) REVERT: H 488 ARG cc_start: 0.8037 (mmt90) cc_final: 0.7694 (mmt180) REVERT: H 489 GLN cc_start: 0.8690 (tt0) cc_final: 0.8121 (tt0) REVERT: H 500 GLU cc_start: 0.8089 (mp0) cc_final: 0.7686 (pm20) REVERT: H 501 PHE cc_start: 0.8795 (t80) cc_final: 0.8462 (t80) REVERT: I 441 GLN cc_start: 0.8328 (mm-40) cc_final: 0.8110 (mp10) REVERT: I 447 ILE cc_start: 0.8429 (mt) cc_final: 0.8213 (mm) REVERT: I 461 ASP cc_start: 0.8724 (t70) cc_final: 0.8113 (t70) REVERT: I 479 THR cc_start: 0.8851 (m) cc_final: 0.8504 (p) REVERT: I 484 THR cc_start: 0.9068 (t) cc_final: 0.8647 (m) REVERT: I 489 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7920 (tm-30) REVERT: I 503 LYS cc_start: 0.8909 (ptmt) cc_final: 0.8605 (pttp) REVERT: I 515 MET cc_start: 0.7173 (tpp) cc_final: 0.6104 (mmm) REVERT: J 430 THR cc_start: 0.6992 (m) cc_final: 0.6761 (t) REVERT: J 445 GLU cc_start: 0.8545 (mp0) cc_final: 0.7838 (mp0) REVERT: J 449 ASN cc_start: 0.9189 (m-40) cc_final: 0.8879 (m-40) REVERT: J 451 MET cc_start: 0.8782 (tpt) cc_final: 0.8280 (tpp) REVERT: J 453 GLU cc_start: 0.9225 (tp30) cc_final: 0.8762 (tp30) REVERT: J 457 ASN cc_start: 0.8765 (p0) cc_final: 0.8500 (p0) REVERT: J 469 ILE cc_start: 0.9339 (tt) cc_final: 0.9096 (tt) REVERT: J 470 MET cc_start: 0.9303 (mtm) cc_final: 0.8914 (mtt) REVERT: J 489 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8361 (tm-30) REVERT: J 492 ASP cc_start: 0.9217 (m-30) cc_final: 0.9002 (m-30) REVERT: J 495 ASP cc_start: 0.9323 (m-30) cc_final: 0.9047 (m-30) REVERT: J 500 GLU cc_start: 0.9096 (tp30) cc_final: 0.8706 (tp30) REVERT: K 444 ARG cc_start: 0.7026 (ttm170) cc_final: 0.6435 (ptt180) REVERT: K 450 GLN cc_start: 0.9087 (mm-40) cc_final: 0.8520 (mm110) REVERT: K 453 GLU cc_start: 0.9088 (tm-30) cc_final: 0.8711 (tm-30) REVERT: K 456 LEU cc_start: 0.9096 (tp) cc_final: 0.8830 (tp) REVERT: K 461 ASP cc_start: 0.8658 (t70) cc_final: 0.8428 (t70) REVERT: K 485 SER cc_start: 0.9390 (m) cc_final: 0.9045 (p) REVERT: K 486 LYS cc_start: 0.8770 (mtpt) cc_final: 0.8147 (mtpp) REVERT: K 509 LEU cc_start: 0.8938 (mt) cc_final: 0.8694 (mt) REVERT: K 510 LYS cc_start: 0.9014 (pptt) cc_final: 0.8811 (pptt) REVERT: L 437 GLN cc_start: 0.9464 (pt0) cc_final: 0.9055 (pm20) REVERT: L 441 GLN cc_start: 0.9041 (mt0) cc_final: 0.8686 (tm-30) REVERT: L 442 SER cc_start: 0.9323 (t) cc_final: 0.9072 (p) REVERT: L 460 LEU cc_start: 0.9435 (mp) cc_final: 0.9156 (mp) REVERT: L 469 ILE cc_start: 0.9166 (tt) cc_final: 0.8957 (tt) REVERT: L 472 GLU cc_start: 0.8160 (tt0) cc_final: 0.7812 (tt0) REVERT: L 492 ASP cc_start: 0.9242 (m-30) cc_final: 0.8758 (m-30) REVERT: L 501 PHE cc_start: 0.9058 (t80) cc_final: 0.8818 (t80) REVERT: L 503 LYS cc_start: 0.9366 (mtpp) cc_final: 0.8985 (mtpp) REVERT: L 504 VAL cc_start: 0.9479 (t) cc_final: 0.9275 (m) outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.2599 time to fit residues: 149.2459 Evaluate side-chains 366 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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: 0.0980 chunk 45 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 13 optimal weight: 0.3980 chunk 64 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 overall best weight: 2.0784 ------------------------------------------------------------------------------- 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** B 489 GLN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 GLN D 457 ASN ** D 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 GLN E 507 GLN E 512 ASN F 458 GLN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 ASN H 514 GLN ** I 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN K 514 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 = 0.3445 r_free = 0.3445 target = 0.071500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.057180 restraints weight = 35986.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.059211 restraints weight = 24477.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.060756 restraints weight = 18238.298| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 1.6876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8328 Z= 0.229 Angle : 0.715 9.956 11184 Z= 0.382 Chirality : 0.043 0.171 1332 Planarity : 0.004 0.070 1440 Dihedral : 5.033 20.845 1092 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.11 % Allowed : 2.32 % Favored : 97.57 % 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: -0.09 (0.25), residues: 1020 helix: 0.18 (0.17), residues: 852 sheet: None (None), residues: 0 loop : -0.63 (0.47), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 439 PHE 0.010 0.002 PHE E 501 TYR 0.010 0.001 TYR G 474 ARG 0.005 0.001 ARG A 483 *********************** 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 449 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 448 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 GLN cc_start: 0.8558 (mt0) cc_final: 0.8305 (mt0) REVERT: A 471 LYS cc_start: 0.9095 (ptpp) cc_final: 0.8652 (ttpp) REVERT: A 476 LEU cc_start: 0.9663 (mt) cc_final: 0.9438 (mt) REVERT: A 479 THR cc_start: 0.8848 (t) cc_final: 0.8589 (p) REVERT: A 480 LYS cc_start: 0.9553 (mmtt) cc_final: 0.9220 (mmmt) REVERT: A 488 ARG cc_start: 0.8089 (mtt-85) cc_final: 0.7834 (mtt-85) REVERT: A 489 GLN cc_start: 0.8485 (tm-30) cc_final: 0.8238 (tp40) REVERT: A 500 GLU cc_start: 0.8313 (pm20) cc_final: 0.8017 (pm20) REVERT: A 513 LYS cc_start: 0.9082 (mmpt) cc_final: 0.8869 (mmmt) REVERT: B 458 GLN cc_start: 0.9194 (mp10) cc_final: 0.8877 (pt0) REVERT: B 472 GLU cc_start: 0.9070 (mp0) cc_final: 0.8703 (tt0) REVERT: C 440 ILE cc_start: 0.8786 (mt) cc_final: 0.8560 (mt) REVERT: C 456 LEU cc_start: 0.9476 (tp) cc_final: 0.9207 (tp) REVERT: C 459 SER cc_start: 0.9657 (m) cc_final: 0.9241 (p) REVERT: C 461 ASP cc_start: 0.9020 (m-30) cc_final: 0.8794 (m-30) REVERT: C 470 MET cc_start: 0.8687 (mtp) cc_final: 0.8107 (mtm) REVERT: C 513 LYS cc_start: 0.8797 (mmmt) cc_final: 0.8446 (mmmt) REVERT: C 515 MET cc_start: 0.7050 (tpt) cc_final: 0.6812 (mmt) REVERT: D 441 GLN cc_start: 0.7552 (tp40) cc_final: 0.7351 (tp-100) REVERT: D 458 GLN cc_start: 0.8883 (mp10) cc_final: 0.8355 (pt0) REVERT: D 468 LEU cc_start: 0.9321 (mp) cc_final: 0.8868 (mt) REVERT: D 469 ILE cc_start: 0.9306 (tt) cc_final: 0.9006 (tt) REVERT: D 474 TYR cc_start: 0.9296 (t80) cc_final: 0.8924 (t80) REVERT: D 476 LEU cc_start: 0.9025 (mt) cc_final: 0.8814 (mt) REVERT: D 477 VAL cc_start: 0.8959 (t) cc_final: 0.8748 (t) REVERT: D 478 SER cc_start: 0.9464 (t) cc_final: 0.9252 (p) REVERT: D 479 THR cc_start: 0.8704 (m) cc_final: 0.8419 (p) REVERT: D 480 LYS cc_start: 0.9030 (mmtp) cc_final: 0.8559 (mmmm) REVERT: D 483 ARG cc_start: 0.8728 (mtt180) cc_final: 0.8501 (ttp80) REVERT: D 503 LYS cc_start: 0.9106 (pttm) cc_final: 0.8861 (pttm) REVERT: E 445 GLU cc_start: 0.8936 (pm20) cc_final: 0.8717 (pm20) REVERT: E 446 ASP cc_start: 0.9190 (m-30) cc_final: 0.8854 (m-30) REVERT: E 461 ASP cc_start: 0.8553 (m-30) cc_final: 0.8215 (m-30) REVERT: E 471 LYS cc_start: 0.8805 (tttt) cc_final: 0.8368 (tmtt) REVERT: E 473 ASP cc_start: 0.9001 (m-30) cc_final: 0.8753 (m-30) REVERT: E 480 LYS cc_start: 0.8836 (mtpt) cc_final: 0.8493 (mtpp) REVERT: E 494 THR cc_start: 0.9495 (m) cc_final: 0.9087 (m) REVERT: E 501 PHE cc_start: 0.8751 (t80) cc_final: 0.7815 (t80) REVERT: F 449 ASN cc_start: 0.8341 (m-40) cc_final: 0.7991 (m-40) REVERT: G 467 ASP cc_start: 0.8653 (t70) cc_final: 0.8437 (t70) REVERT: G 475 GLU cc_start: 0.7628 (mp0) cc_final: 0.6626 (tm-30) REVERT: G 485 SER cc_start: 0.8434 (m) cc_final: 0.8149 (m) REVERT: G 500 GLU cc_start: 0.7558 (pt0) cc_final: 0.7176 (pm20) REVERT: G 503 LYS cc_start: 0.9170 (ptpp) cc_final: 0.8804 (pttp) REVERT: H 446 ASP cc_start: 0.8898 (m-30) cc_final: 0.8649 (m-30) REVERT: H 460 LEU cc_start: 0.9574 (mp) cc_final: 0.9362 (mp) REVERT: H 470 MET cc_start: 0.8857 (mpp) cc_final: 0.8069 (mpp) REVERT: H 480 LYS cc_start: 0.8537 (ptpp) cc_final: 0.8253 (ptpp) REVERT: H 488 ARG cc_start: 0.8180 (mmt90) cc_final: 0.7550 (mmt90) REVERT: H 489 GLN cc_start: 0.8439 (tt0) cc_final: 0.8078 (tt0) REVERT: H 495 ASP cc_start: 0.9560 (m-30) cc_final: 0.9357 (m-30) REVERT: H 500 GLU cc_start: 0.8211 (mp0) cc_final: 0.7763 (pm20) REVERT: H 501 PHE cc_start: 0.8988 (t80) cc_final: 0.8518 (t80) REVERT: H 505 ILE cc_start: 0.9309 (mm) cc_final: 0.8903 (mm) REVERT: H 507 GLN cc_start: 0.9017 (mp10) cc_final: 0.8531 (mp10) REVERT: I 447 ILE cc_start: 0.8464 (mt) cc_final: 0.8240 (mm) REVERT: I 461 ASP cc_start: 0.8867 (t70) cc_final: 0.8292 (t70) REVERT: I 475 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8605 (mt-10) REVERT: I 479 THR cc_start: 0.8998 (m) cc_final: 0.8743 (p) REVERT: I 484 THR cc_start: 0.9315 (t) cc_final: 0.8992 (m) REVERT: I 515 MET cc_start: 0.7250 (tpp) cc_final: 0.6596 (tpp) REVERT: J 445 GLU cc_start: 0.8607 (mp0) cc_final: 0.8029 (mp0) REVERT: J 449 ASN cc_start: 0.9282 (m-40) cc_final: 0.9039 (m-40) REVERT: J 451 MET cc_start: 0.9007 (tpt) cc_final: 0.8502 (tpp) REVERT: J 453 GLU cc_start: 0.9271 (tp30) cc_final: 0.8787 (tp30) REVERT: J 457 ASN cc_start: 0.8871 (p0) cc_final: 0.8670 (p0) REVERT: J 458 GLN cc_start: 0.9204 (tm-30) cc_final: 0.8990 (tm-30) REVERT: J 470 MET cc_start: 0.9146 (mtm) cc_final: 0.8589 (mtt) REVERT: J 489 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8634 (tm-30) REVERT: J 495 ASP cc_start: 0.9417 (m-30) cc_final: 0.9158 (m-30) REVERT: J 499 GLU cc_start: 0.8456 (pp20) cc_final: 0.7950 (tm-30) REVERT: J 500 GLU cc_start: 0.9111 (tp30) cc_final: 0.8899 (tp30) REVERT: J 503 LYS cc_start: 0.9211 (pptt) cc_final: 0.8886 (ptpp) REVERT: K 444 ARG cc_start: 0.7160 (ttm170) cc_final: 0.6409 (ptt-90) REVERT: K 456 LEU cc_start: 0.9409 (tp) cc_final: 0.9141 (tp) REVERT: K 489 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8564 (tm-30) REVERT: L 441 GLN cc_start: 0.9280 (mt0) cc_final: 0.8917 (tm-30) REVERT: L 460 LEU cc_start: 0.9479 (mp) cc_final: 0.9188 (mp) REVERT: L 469 ILE cc_start: 0.9118 (tt) cc_final: 0.8874 (tt) REVERT: L 472 GLU cc_start: 0.8119 (tt0) cc_final: 0.7869 (tt0) REVERT: L 480 LYS cc_start: 0.9403 (mttm) cc_final: 0.9134 (mtpt) REVERT: L 486 LYS cc_start: 0.9323 (mttp) cc_final: 0.8817 (mtmm) REVERT: L 489 GLN cc_start: 0.9338 (mm110) cc_final: 0.9117 (mm-40) REVERT: L 492 ASP cc_start: 0.9359 (m-30) cc_final: 0.8992 (m-30) REVERT: L 501 PHE cc_start: 0.9059 (t80) cc_final: 0.8741 (t80) REVERT: L 503 LYS cc_start: 0.9440 (mtpp) cc_final: 0.9080 (mtpp) outliers start: 1 outliers final: 0 residues processed: 449 average time/residue: 0.2462 time to fit residues: 142.1074 Evaluate side-chains 372 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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: 5.9990 chunk 24 optimal weight: 20.0000 chunk 35 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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** B 457 ASN ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 457 ASN E 458 GLN E 512 ASN ** F 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 457 ASN F 458 GLN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 ASN G 514 GLN ** H 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 512 ASN ** I 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN L 512 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.066215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.053029 restraints weight = 36685.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.054962 restraints weight = 24026.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.056442 restraints weight = 17621.137| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 1.8521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8328 Z= 0.296 Angle : 0.775 11.078 11184 Z= 0.414 Chirality : 0.043 0.157 1332 Planarity : 0.005 0.076 1440 Dihedral : 5.324 24.054 1092 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % 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: -0.34 (0.25), residues: 1020 helix: 0.05 (0.17), residues: 852 sheet: None (None), residues: 0 loop : -0.95 (0.47), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 439 PHE 0.013 0.002 PHE E 501 TYR 0.016 0.002 TYR H 474 ARG 0.010 0.001 ARG I 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 451 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 451 time to evaluate : 1.063 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 445 GLU cc_start: 0.8932 (pm20) cc_final: 0.8696 (pm20) REVERT: A 446 ASP cc_start: 0.8998 (t0) cc_final: 0.8701 (t0) REVERT: A 461 ASP cc_start: 0.9053 (m-30) cc_final: 0.8730 (t70) REVERT: A 476 LEU cc_start: 0.9698 (mt) cc_final: 0.9426 (mp) REVERT: A 488 ARG cc_start: 0.8150 (mtt-85) cc_final: 0.7890 (mtp85) REVERT: A 489 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8337 (tp40) REVERT: A 500 GLU cc_start: 0.8397 (pm20) cc_final: 0.8034 (pm20) REVERT: B 443 LYS cc_start: 0.8894 (ttpt) cc_final: 0.8506 (tppt) REVERT: B 458 GLN cc_start: 0.9109 (mp10) cc_final: 0.8889 (pt0) REVERT: B 492 ASP cc_start: 0.8984 (m-30) cc_final: 0.8660 (m-30) REVERT: B 499 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8080 (mm-30) REVERT: C 461 ASP cc_start: 0.9014 (m-30) cc_final: 0.8554 (m-30) REVERT: C 470 MET cc_start: 0.8677 (mtp) cc_final: 0.6157 (mtm) REVERT: C 473 ASP cc_start: 0.9405 (m-30) cc_final: 0.9154 (m-30) REVERT: C 475 GLU cc_start: 0.8931 (tt0) cc_final: 0.8711 (tt0) REVERT: C 479 THR cc_start: 0.9247 (m) cc_final: 0.9044 (p) REVERT: C 495 ASP cc_start: 0.9313 (t70) cc_final: 0.8943 (t0) REVERT: C 513 LYS cc_start: 0.8774 (mmmt) cc_final: 0.8322 (mmmt) REVERT: C 515 MET cc_start: 0.7007 (tpt) cc_final: 0.6647 (mmt) REVERT: D 441 GLN cc_start: 0.8575 (tp40) cc_final: 0.8180 (tp-100) REVERT: D 461 ASP cc_start: 0.9259 (m-30) cc_final: 0.8770 (t70) REVERT: D 466 ARG cc_start: 0.9055 (mpp80) cc_final: 0.8841 (mpp80) REVERT: D 468 LEU cc_start: 0.9368 (mp) cc_final: 0.9038 (mt) REVERT: D 474 TYR cc_start: 0.9494 (t80) cc_final: 0.9183 (t80) REVERT: D 478 SER cc_start: 0.9617 (t) cc_final: 0.9341 (p) REVERT: D 479 THR cc_start: 0.9065 (m) cc_final: 0.8820 (p) REVERT: D 480 LYS cc_start: 0.9214 (mmtp) cc_final: 0.8804 (mmmm) REVERT: D 500 GLU cc_start: 0.8102 (pp20) cc_final: 0.7769 (pm20) REVERT: E 441 GLN cc_start: 0.9001 (mt0) cc_final: 0.8736 (mp10) REVERT: E 443 LYS cc_start: 0.9404 (ptpt) cc_final: 0.9036 (ptpp) REVERT: E 445 GLU cc_start: 0.8964 (pm20) cc_final: 0.8671 (pm20) REVERT: E 446 ASP cc_start: 0.9259 (m-30) cc_final: 0.8847 (m-30) REVERT: E 461 ASP cc_start: 0.8403 (m-30) cc_final: 0.8029 (m-30) REVERT: E 471 LYS cc_start: 0.8896 (tttt) cc_final: 0.8547 (tmtt) REVERT: E 473 ASP cc_start: 0.8828 (m-30) cc_final: 0.8531 (m-30) REVERT: E 476 LEU cc_start: 0.9153 (mt) cc_final: 0.8067 (mt) REVERT: E 480 LYS cc_start: 0.9038 (mtpt) cc_final: 0.8635 (mtpp) REVERT: E 489 GLN cc_start: 0.8767 (mp10) cc_final: 0.8419 (mp10) REVERT: E 495 ASP cc_start: 0.9197 (m-30) cc_final: 0.8926 (m-30) REVERT: F 446 ASP cc_start: 0.9142 (t70) cc_final: 0.8819 (t0) REVERT: F 461 ASP cc_start: 0.9276 (t70) cc_final: 0.8816 (m-30) REVERT: G 446 ASP cc_start: 0.8844 (m-30) cc_final: 0.8455 (m-30) REVERT: G 471 LYS cc_start: 0.6948 (mmpt) cc_final: 0.6726 (tppp) REVERT: G 475 GLU cc_start: 0.8028 (mp0) cc_final: 0.7002 (tm-30) REVERT: G 489 GLN cc_start: 0.8496 (mp10) cc_final: 0.7854 (mp10) REVERT: G 497 GLN cc_start: 0.5853 (mm-40) cc_final: 0.5337 (tp40) REVERT: H 470 MET cc_start: 0.8922 (mpp) cc_final: 0.7118 (mtt) REVERT: H 473 ASP cc_start: 0.8657 (m-30) cc_final: 0.8431 (m-30) REVERT: H 480 LYS cc_start: 0.8554 (ptpp) cc_final: 0.8350 (ptpp) REVERT: H 489 GLN cc_start: 0.8375 (tt0) cc_final: 0.8041 (tt0) REVERT: H 500 GLU cc_start: 0.8265 (mp0) cc_final: 0.7917 (pm20) REVERT: H 501 PHE cc_start: 0.9093 (t80) cc_final: 0.8514 (t80) REVERT: H 505 ILE cc_start: 0.9338 (mm) cc_final: 0.9107 (mm) REVERT: H 507 GLN cc_start: 0.8982 (mp10) cc_final: 0.8734 (mp10) REVERT: I 458 GLN cc_start: 0.9208 (mt0) cc_final: 0.8990 (mt0) REVERT: I 478 SER cc_start: 0.9684 (t) cc_final: 0.9468 (p) REVERT: I 479 THR cc_start: 0.9461 (m) cc_final: 0.9248 (p) REVERT: I 480 LYS cc_start: 0.9179 (mmtp) cc_final: 0.8914 (mttt) REVERT: I 486 LYS cc_start: 0.9286 (mtpp) cc_final: 0.9007 (mttp) REVERT: I 499 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8095 (mm-30) REVERT: J 445 GLU cc_start: 0.8742 (mp0) cc_final: 0.8251 (mp0) REVERT: J 449 ASN cc_start: 0.9280 (m-40) cc_final: 0.9005 (m-40) REVERT: J 451 MET cc_start: 0.9201 (tpt) cc_final: 0.8891 (tpp) REVERT: J 453 GLU cc_start: 0.9353 (tp30) cc_final: 0.8780 (tp30) REVERT: J 457 ASN cc_start: 0.8923 (p0) cc_final: 0.8610 (p0) REVERT: J 470 MET cc_start: 0.9187 (mtm) cc_final: 0.8827 (mtt) REVERT: J 472 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8645 (mt-10) REVERT: J 501 PHE cc_start: 0.9162 (t80) cc_final: 0.8257 (t80) REVERT: K 444 ARG cc_start: 0.7315 (ttm170) cc_final: 0.6629 (ptt-90) REVERT: K 456 LEU cc_start: 0.9595 (tp) cc_final: 0.9366 (tp) REVERT: K 470 MET cc_start: 0.2198 (ptt) cc_final: 0.1782 (mtt) REVERT: K 471 LYS cc_start: 0.9136 (mmmm) cc_final: 0.8592 (tttm) REVERT: L 445 GLU cc_start: 0.8975 (pm20) cc_final: 0.8652 (pm20) REVERT: L 446 ASP cc_start: 0.8971 (m-30) cc_final: 0.8709 (m-30) REVERT: L 460 LEU cc_start: 0.9556 (mp) cc_final: 0.9267 (mp) REVERT: L 469 ILE cc_start: 0.9163 (tt) cc_final: 0.8897 (tt) REVERT: L 476 LEU cc_start: 0.9538 (mt) cc_final: 0.9335 (mt) REVERT: L 486 LYS cc_start: 0.9422 (mttp) cc_final: 0.9171 (mtmm) REVERT: L 492 ASP cc_start: 0.9266 (m-30) cc_final: 0.8908 (m-30) REVERT: L 501 PHE cc_start: 0.9046 (t80) cc_final: 0.8729 (t80) REVERT: L 503 LYS cc_start: 0.9478 (mtpp) cc_final: 0.9141 (mtpp) outliers start: 0 outliers final: 0 residues processed: 451 average time/residue: 0.2430 time to fit residues: 141.5233 Evaluate side-chains 377 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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: 5.9990 chunk 87 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN C 458 GLN ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 449 ASN D 457 ASN D 458 GLN E 458 GLN E 512 ASN F 438 GLN ** F 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 458 GLN ** 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 512 ASN ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN L 489 GLN L 512 ASN L 514 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.063004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.050429 restraints weight = 38555.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.052430 restraints weight = 24509.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.053845 restraints weight = 17524.277| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 2.0047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8328 Z= 0.319 Angle : 0.825 10.330 11184 Z= 0.440 Chirality : 0.046 0.172 1332 Planarity : 0.005 0.079 1440 Dihedral : 5.497 24.029 1092 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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: -0.83 (0.24), residues: 1020 helix: -0.27 (0.16), residues: 852 sheet: None (None), residues: 0 loop : -1.25 (0.47), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 439 PHE 0.016 0.003 PHE A 501 TYR 0.030 0.003 TYR K 474 ARG 0.009 0.001 ARG H 466 *********************** 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 466 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 466 time to evaluate : 1.014 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 461 ASP cc_start: 0.9070 (m-30) cc_final: 0.8859 (t70) REVERT: A 470 MET cc_start: 0.9005 (mtt) cc_final: 0.7483 (mtt) REVERT: A 472 GLU cc_start: 0.9085 (mp0) cc_final: 0.8604 (mp0) REVERT: A 476 LEU cc_start: 0.9658 (mt) cc_final: 0.9416 (mp) REVERT: A 488 ARG cc_start: 0.8012 (mtt-85) cc_final: 0.7752 (mtt-85) REVERT: A 489 GLN cc_start: 0.8450 (tm-30) cc_final: 0.8143 (tp40) REVERT: A 500 GLU cc_start: 0.8404 (pm20) cc_final: 0.8004 (pm20) REVERT: A 513 LYS cc_start: 0.9177 (mmpt) cc_final: 0.8967 (mmmt) REVERT: B 443 LYS cc_start: 0.8796 (ttpt) cc_final: 0.8378 (tppt) REVERT: B 453 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8894 (tm-30) REVERT: B 469 ILE cc_start: 0.9297 (tt) cc_final: 0.9087 (tt) REVERT: B 480 LYS cc_start: 0.9257 (mmmm) cc_final: 0.8738 (mmmt) REVERT: B 492 ASP cc_start: 0.9038 (m-30) cc_final: 0.8798 (m-30) REVERT: B 500 GLU cc_start: 0.8471 (pm20) cc_final: 0.8249 (pm20) REVERT: B 503 LYS cc_start: 0.9487 (pttm) cc_final: 0.9167 (ptpp) REVERT: C 446 ASP cc_start: 0.9158 (m-30) cc_final: 0.8789 (t0) REVERT: C 449 ASN cc_start: 0.8734 (m-40) cc_final: 0.8484 (m-40) REVERT: C 461 ASP cc_start: 0.8999 (m-30) cc_final: 0.8659 (m-30) REVERT: C 468 LEU cc_start: 0.9354 (mp) cc_final: 0.9145 (mm) REVERT: C 471 LYS cc_start: 0.8811 (tmtt) cc_final: 0.8492 (tmtt) REVERT: C 473 ASP cc_start: 0.9426 (m-30) cc_final: 0.9213 (m-30) REVERT: C 513 LYS cc_start: 0.8786 (mmmt) cc_final: 0.8323 (mmmt) REVERT: C 515 MET cc_start: 0.6815 (tpt) cc_final: 0.6498 (mmt) REVERT: D 441 GLN cc_start: 0.8631 (tp40) cc_final: 0.8160 (tm-30) REVERT: D 461 ASP cc_start: 0.9254 (m-30) cc_final: 0.8849 (t70) REVERT: D 478 SER cc_start: 0.9652 (t) cc_final: 0.9398 (p) REVERT: D 480 LYS cc_start: 0.9242 (mmtp) cc_final: 0.8902 (mmmm) REVERT: D 486 LYS cc_start: 0.9183 (mttm) cc_final: 0.8937 (mttm) REVERT: D 491 LEU cc_start: 0.9519 (mt) cc_final: 0.9254 (mt) REVERT: D 500 GLU cc_start: 0.8370 (pp20) cc_final: 0.8032 (pm20) REVERT: D 507 GLN cc_start: 0.9242 (pp30) cc_final: 0.8996 (tp-100) REVERT: E 441 GLN cc_start: 0.8963 (mt0) cc_final: 0.8717 (mp10) REVERT: E 443 LYS cc_start: 0.9458 (ptpt) cc_final: 0.8448 (ptpp) REVERT: E 446 ASP cc_start: 0.9285 (m-30) cc_final: 0.8837 (p0) REVERT: E 476 LEU cc_start: 0.8904 (mt) cc_final: 0.8406 (mt) REVERT: E 480 LYS cc_start: 0.9087 (mtpt) cc_final: 0.8805 (mtpp) REVERT: E 483 ARG cc_start: 0.8359 (ttt180) cc_final: 0.8102 (ttt180) REVERT: E 489 GLN cc_start: 0.8818 (mp10) cc_final: 0.8440 (mp10) REVERT: E 495 ASP cc_start: 0.9137 (m-30) cc_final: 0.8817 (m-30) REVERT: E 501 PHE cc_start: 0.8952 (t80) cc_final: 0.8423 (t80) REVERT: F 446 ASP cc_start: 0.9112 (t70) cc_final: 0.8821 (t0) REVERT: F 482 THR cc_start: 0.8224 (t) cc_final: 0.7890 (p) REVERT: G 475 GLU cc_start: 0.8199 (mp0) cc_final: 0.7146 (tm-30) REVERT: G 485 SER cc_start: 0.8725 (m) cc_final: 0.8335 (p) REVERT: G 489 GLN cc_start: 0.8578 (mp10) cc_final: 0.8126 (mp10) REVERT: G 509 LEU cc_start: 0.9290 (tp) cc_final: 0.8992 (tt) REVERT: H 451 MET cc_start: 0.9371 (tpp) cc_final: 0.9123 (tpp) REVERT: H 470 MET cc_start: 0.8730 (mpp) cc_final: 0.7763 (mtm) REVERT: H 473 ASP cc_start: 0.9041 (m-30) cc_final: 0.8775 (m-30) REVERT: H 476 LEU cc_start: 0.9462 (mt) cc_final: 0.9235 (mt) REVERT: H 478 SER cc_start: 0.9426 (m) cc_final: 0.9194 (p) REVERT: H 480 LYS cc_start: 0.8643 (ptpp) cc_final: 0.8193 (ptpp) REVERT: H 489 GLN cc_start: 0.8467 (tt0) cc_final: 0.8126 (tt0) REVERT: H 500 GLU cc_start: 0.8533 (mp0) cc_final: 0.8118 (pm20) REVERT: H 501 PHE cc_start: 0.9087 (t80) cc_final: 0.8494 (t80) REVERT: I 486 LYS cc_start: 0.9300 (mtpp) cc_final: 0.8917 (mttm) REVERT: I 491 LEU cc_start: 0.9451 (mt) cc_final: 0.9208 (mt) REVERT: I 515 MET cc_start: 0.5775 (tpt) cc_final: 0.4796 (mmm) REVERT: J 445 GLU cc_start: 0.8712 (mp0) cc_final: 0.8150 (mp0) REVERT: J 449 ASN cc_start: 0.9212 (m-40) cc_final: 0.8888 (m-40) REVERT: J 451 MET cc_start: 0.9185 (tpt) cc_final: 0.8695 (tpp) REVERT: J 453 GLU cc_start: 0.9396 (tp30) cc_final: 0.8860 (tp30) REVERT: J 457 ASN cc_start: 0.8894 (p0) cc_final: 0.8530 (p0) REVERT: J 469 ILE cc_start: 0.9084 (tt) cc_final: 0.8876 (tt) REVERT: J 470 MET cc_start: 0.9094 (mtm) cc_final: 0.7835 (mtt) REVERT: J 472 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8690 (mt-10) REVERT: J 494 THR cc_start: 0.9613 (m) cc_final: 0.9301 (m) REVERT: J 500 GLU cc_start: 0.9178 (tp30) cc_final: 0.8608 (pm20) REVERT: J 501 PHE cc_start: 0.9276 (t80) cc_final: 0.8413 (t80) REVERT: K 444 ARG cc_start: 0.7595 (ttm170) cc_final: 0.6791 (ptt180) REVERT: K 486 LYS cc_start: 0.9344 (mtpt) cc_final: 0.9057 (mtpp) REVERT: L 441 GLN cc_start: 0.9104 (tt0) cc_final: 0.8593 (tp-100) REVERT: L 445 GLU cc_start: 0.8988 (pm20) cc_final: 0.8659 (pm20) REVERT: L 446 ASP cc_start: 0.9094 (m-30) cc_final: 0.8803 (m-30) REVERT: L 460 LEU cc_start: 0.9572 (mp) cc_final: 0.9270 (mp) REVERT: L 468 LEU cc_start: 0.9315 (mt) cc_final: 0.9061 (mt) REVERT: L 469 ILE cc_start: 0.9239 (tt) cc_final: 0.8976 (tt) REVERT: L 486 LYS cc_start: 0.9459 (mttp) cc_final: 0.9228 (mtmm) REVERT: L 501 PHE cc_start: 0.9111 (t80) cc_final: 0.8743 (t80) outliers start: 0 outliers final: 0 residues processed: 466 average time/residue: 0.2399 time to fit residues: 144.4790 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 : 1.134 ------------------------------------------------------------------------------- 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: 2.9990 chunk 82 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 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 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 GLN B 441 GLN B 450 GLN ** B 489 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 449 ASN E 458 GLN E 507 GLN E 512 ASN F 441 GLN ** 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 512 ASN ** I 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 489 GLN ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 458 GLN K 512 ASN L 512 ASN L 514 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.063970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.050970 restraints weight = 38183.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.052896 restraints weight = 24611.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.054372 restraints weight = 18001.409| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 2.0449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8328 Z= 0.248 Angle : 0.795 8.129 11184 Z= 0.423 Chirality : 0.044 0.177 1332 Planarity : 0.005 0.071 1440 Dihedral : 5.441 29.642 1092 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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: -0.55 (0.25), residues: 1020 helix: -0.08 (0.17), residues: 852 sheet: None (None), residues: 0 loop : -1.13 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 439 PHE 0.012 0.002 PHE E 501 TYR 0.021 0.002 TYR I 474 ARG 0.016 0.001 ARG C 488 *********************** 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 478 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 478 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 GLN cc_start: 0.8788 (mt0) cc_final: 0.8455 (pt0) REVERT: A 458 GLN cc_start: 0.9117 (pt0) cc_final: 0.8762 (pt0) REVERT: A 461 ASP cc_start: 0.9060 (m-30) cc_final: 0.8787 (t70) REVERT: A 470 MET cc_start: 0.8813 (mtt) cc_final: 0.8385 (mtt) REVERT: A 472 GLU cc_start: 0.9170 (mp0) cc_final: 0.8648 (mp0) REVERT: A 480 LYS cc_start: 0.9430 (mmmt) cc_final: 0.9155 (mmmt) REVERT: A 489 GLN cc_start: 0.8450 (tm-30) cc_final: 0.8159 (tp40) REVERT: A 500 GLU cc_start: 0.8389 (pm20) cc_final: 0.8078 (pm20) REVERT: A 501 PHE cc_start: 0.9324 (t80) cc_final: 0.8894 (t80) REVERT: B 486 LYS cc_start: 0.9506 (mttp) cc_final: 0.8984 (mttp) REVERT: B 489 GLN cc_start: 0.8895 (mp10) cc_final: 0.8651 (mp10) REVERT: B 499 GLU cc_start: 0.8446 (mm-30) cc_final: 0.7736 (mm-30) REVERT: B 500 GLU cc_start: 0.8649 (pm20) cc_final: 0.8390 (pm20) REVERT: B 503 LYS cc_start: 0.9441 (pttm) cc_final: 0.9071 (ptpp) REVERT: C 441 GLN cc_start: 0.8286 (mm-40) cc_final: 0.7820 (tp-100) REVERT: C 446 ASP cc_start: 0.9150 (m-30) cc_final: 0.8761 (t0) REVERT: C 449 ASN cc_start: 0.8672 (m-40) cc_final: 0.8417 (m-40) REVERT: C 461 ASP cc_start: 0.9081 (m-30) cc_final: 0.8755 (m-30) REVERT: C 468 LEU cc_start: 0.9374 (mp) cc_final: 0.9096 (mm) REVERT: C 470 MET cc_start: 0.8829 (mtp) cc_final: 0.8233 (mtm) REVERT: C 471 LYS cc_start: 0.8882 (tmtt) cc_final: 0.8615 (tmtt) REVERT: C 472 GLU cc_start: 0.9275 (mp0) cc_final: 0.8746 (mp0) REVERT: C 503 LYS cc_start: 0.9450 (ttmt) cc_final: 0.9203 (ptpp) REVERT: D 441 GLN cc_start: 0.8536 (tp40) cc_final: 0.8123 (tm-30) REVERT: D 461 ASP cc_start: 0.9159 (m-30) cc_final: 0.8915 (t70) REVERT: D 470 MET cc_start: 0.8373 (ptp) cc_final: 0.8163 (ptp) REVERT: D 478 SER cc_start: 0.9615 (t) cc_final: 0.9388 (p) REVERT: D 480 LYS cc_start: 0.9274 (mmtp) cc_final: 0.8929 (mmmm) REVERT: E 441 GLN cc_start: 0.8935 (mt0) cc_final: 0.8658 (mp10) REVERT: E 446 ASP cc_start: 0.9292 (m-30) cc_final: 0.8826 (p0) REVERT: E 451 MET cc_start: 0.9280 (tpp) cc_final: 0.9045 (tpp) REVERT: E 473 ASP cc_start: 0.8642 (m-30) cc_final: 0.8433 (m-30) REVERT: E 476 LEU cc_start: 0.8603 (mt) cc_final: 0.8090 (mt) REVERT: E 480 LYS cc_start: 0.9100 (mtpt) cc_final: 0.8720 (mtpp) REVERT: E 489 GLN cc_start: 0.8853 (mp10) cc_final: 0.8501 (mp10) REVERT: E 492 ASP cc_start: 0.9357 (m-30) cc_final: 0.9141 (m-30) REVERT: E 501 PHE cc_start: 0.8955 (t80) cc_final: 0.8574 (t80) REVERT: F 446 ASP cc_start: 0.8979 (t70) cc_final: 0.8746 (t0) REVERT: F 460 LEU cc_start: 0.9458 (pp) cc_final: 0.9197 (pp) REVERT: F 461 ASP cc_start: 0.9405 (t70) cc_final: 0.8772 (m-30) REVERT: G 445 GLU cc_start: 0.8383 (pm20) cc_final: 0.7731 (pm20) REVERT: G 446 ASP cc_start: 0.8615 (m-30) cc_final: 0.8043 (m-30) REVERT: G 461 ASP cc_start: 0.9175 (m-30) cc_final: 0.8597 (t70) REVERT: G 464 LEU cc_start: 0.9491 (mt) cc_final: 0.9246 (mt) REVERT: G 465 SER cc_start: 0.8819 (m) cc_final: 0.8438 (p) REVERT: G 471 LYS cc_start: 0.7832 (mmpt) cc_final: 0.7627 (mmmm) REVERT: G 475 GLU cc_start: 0.8094 (mp0) cc_final: 0.7482 (tm-30) REVERT: G 485 SER cc_start: 0.8777 (m) cc_final: 0.8407 (m) REVERT: G 488 ARG cc_start: 0.8523 (mmm-85) cc_final: 0.8148 (mmm-85) REVERT: G 489 GLN cc_start: 0.8428 (mp10) cc_final: 0.8034 (mp10) REVERT: H 451 MET cc_start: 0.9448 (tpp) cc_final: 0.9197 (tpp) REVERT: H 466 ARG cc_start: 0.8322 (mtm-85) cc_final: 0.7490 (mtm-85) REVERT: H 470 MET cc_start: 0.8585 (mpp) cc_final: 0.6799 (mpp) REVERT: H 473 ASP cc_start: 0.9043 (m-30) cc_final: 0.8533 (m-30) REVERT: H 476 LEU cc_start: 0.9449 (mt) cc_final: 0.8858 (mt) REVERT: H 480 LYS cc_start: 0.8552 (ptpp) cc_final: 0.8119 (ptpp) REVERT: H 489 GLN cc_start: 0.8455 (tt0) cc_final: 0.8144 (tt0) REVERT: H 491 LEU cc_start: 0.9605 (mm) cc_final: 0.9340 (mp) REVERT: H 496 ILE cc_start: 0.8343 (tp) cc_final: 0.8042 (tp) REVERT: H 500 GLU cc_start: 0.8497 (mp0) cc_final: 0.8140 (pm20) REVERT: H 501 PHE cc_start: 0.9069 (t80) cc_final: 0.8415 (t80) REVERT: I 480 LYS cc_start: 0.9027 (mttt) cc_final: 0.8531 (mttt) REVERT: I 486 LYS cc_start: 0.9348 (mtpp) cc_final: 0.9089 (mttm) REVERT: I 499 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7969 (mm-30) REVERT: I 515 MET cc_start: 0.5743 (tpt) cc_final: 0.4748 (mmm) REVERT: J 445 GLU cc_start: 0.8751 (mp0) cc_final: 0.8289 (mp0) REVERT: J 449 ASN cc_start: 0.9186 (m-40) cc_final: 0.8779 (m-40) REVERT: J 451 MET cc_start: 0.9221 (tpt) cc_final: 0.8767 (tpp) REVERT: J 453 GLU cc_start: 0.9371 (tp30) cc_final: 0.8879 (tp30) REVERT: J 457 ASN cc_start: 0.8854 (p0) cc_final: 0.8532 (p0) REVERT: J 458 GLN cc_start: 0.9413 (pt0) cc_final: 0.9011 (pt0) REVERT: J 470 MET cc_start: 0.8989 (mtm) cc_final: 0.8633 (mtt) REVERT: J 489 GLN cc_start: 0.9001 (tm-30) cc_final: 0.8738 (tm-30) REVERT: J 501 PHE cc_start: 0.9250 (t80) cc_final: 0.8614 (t80) REVERT: K 444 ARG cc_start: 0.7036 (ttm170) cc_final: 0.6801 (ptt180) REVERT: K 470 MET cc_start: 0.7898 (mtt) cc_final: 0.7559 (mtt) REVERT: K 478 SER cc_start: 0.9571 (t) cc_final: 0.9368 (p) REVERT: K 486 LYS cc_start: 0.9373 (mtpt) cc_final: 0.9164 (mtpp) REVERT: K 489 GLN cc_start: 0.8855 (tm-30) cc_final: 0.8569 (tm-30) REVERT: L 441 GLN cc_start: 0.9086 (tt0) cc_final: 0.8513 (tp-100) REVERT: L 445 GLU cc_start: 0.9005 (pm20) cc_final: 0.8733 (pm20) REVERT: L 446 ASP cc_start: 0.9082 (m-30) cc_final: 0.8799 (m-30) REVERT: L 460 LEU cc_start: 0.9569 (mp) cc_final: 0.9290 (mp) REVERT: L 468 LEU cc_start: 0.9313 (mt) cc_final: 0.9052 (mt) REVERT: L 469 ILE cc_start: 0.8993 (tt) cc_final: 0.8724 (tt) REVERT: L 475 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8491 (tt0) REVERT: L 486 LYS cc_start: 0.9451 (mttp) cc_final: 0.9207 (mtmm) REVERT: L 492 ASP cc_start: 0.9158 (m-30) cc_final: 0.8790 (m-30) REVERT: L 501 PHE cc_start: 0.9102 (t80) cc_final: 0.8739 (t80) REVERT: L 503 LYS cc_start: 0.9430 (mtpp) cc_final: 0.9219 (mtmt) outliers start: 0 outliers final: 0 residues processed: 478 average time/residue: 0.2394 time to fit residues: 149.7128 Evaluate side-chains 415 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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: 30.0000 chunk 76 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 7 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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** B 489 GLN C 489 GLN ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 449 ASN D 458 GLN ** D 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 512 ASN F 438 GLN ** F 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 ASN H 449 ASN I 438 GLN ** I 450 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 458 GLN K 437 GLN K 512 ASN L 489 GLN L 512 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.064875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.051651 restraints weight = 37199.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.053587 restraints weight = 24370.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.055044 restraints weight = 17875.419| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 2.0670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8328 Z= 0.261 Angle : 0.828 8.356 11184 Z= 0.439 Chirality : 0.046 0.223 1332 Planarity : 0.006 0.089 1440 Dihedral : 5.373 28.145 1092 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.21 % Allowed : 0.95 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.25), residues: 1020 helix: -0.18 (0.17), residues: 852 sheet: None (None), residues: 0 loop : -1.21 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP A 439 PHE 0.026 0.003 PHE G 501 TYR 0.011 0.002 TYR L 474 ARG 0.008 0.001 ARG B 488 ********************** 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 468 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 466 time to evaluate : 0.999 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 445 GLU cc_start: 0.8894 (pm20) cc_final: 0.8645 (pm20) REVERT: A 450 GLN cc_start: 0.8775 (mt0) cc_final: 0.8443 (pt0) REVERT: A 461 ASP cc_start: 0.9023 (m-30) cc_final: 0.8785 (t70) REVERT: A 470 MET cc_start: 0.8913 (mtt) cc_final: 0.8567 (mtt) REVERT: A 472 GLU cc_start: 0.9151 (mp0) cc_final: 0.8710 (mp0) REVERT: A 480 LYS cc_start: 0.9428 (mmmt) cc_final: 0.9116 (mmmt) REVERT: A 489 GLN cc_start: 0.8379 (tm-30) cc_final: 0.8101 (tp40) REVERT: A 501 PHE cc_start: 0.9327 (t80) cc_final: 0.8914 (t80) REVERT: B 480 LYS cc_start: 0.9114 (mmmm) cc_final: 0.8865 (mmmt) REVERT: B 486 LYS cc_start: 0.9505 (mttp) cc_final: 0.9129 (mttp) REVERT: B 499 GLU cc_start: 0.8470 (mm-30) cc_final: 0.7815 (mm-30) REVERT: B 503 LYS cc_start: 0.9118 (pttm) cc_final: 0.8753 (ptpp) REVERT: C 446 ASP cc_start: 0.9169 (m-30) cc_final: 0.8802 (t0) REVERT: C 449 ASN cc_start: 0.8592 (m-40) cc_final: 0.8339 (m-40) REVERT: C 461 ASP cc_start: 0.9135 (m-30) cc_final: 0.8925 (m-30) REVERT: C 468 LEU cc_start: 0.9296 (mp) cc_final: 0.9024 (mm) REVERT: C 470 MET cc_start: 0.8740 (mtp) cc_final: 0.8131 (mtm) REVERT: C 471 LYS cc_start: 0.8727 (tmtt) cc_final: 0.8369 (tmtt) REVERT: C 472 GLU cc_start: 0.9322 (mp0) cc_final: 0.8788 (mp0) REVERT: C 489 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7561 (mp10) REVERT: D 441 GLN cc_start: 0.8502 (tp40) cc_final: 0.8043 (tm-30) REVERT: D 449 ASN cc_start: 0.8722 (m-40) cc_final: 0.8497 (m110) REVERT: D 461 ASP cc_start: 0.9167 (m-30) cc_final: 0.8868 (t70) REVERT: D 472 GLU cc_start: 0.9139 (mp0) cc_final: 0.8855 (tt0) REVERT: D 480 LYS cc_start: 0.9325 (mmtp) cc_final: 0.9029 (mmmm) REVERT: D 491 LEU cc_start: 0.9314 (mp) cc_final: 0.9058 (mp) REVERT: D 495 ASP cc_start: 0.9094 (m-30) cc_final: 0.8882 (m-30) REVERT: E 441 GLN cc_start: 0.8942 (mt0) cc_final: 0.8680 (mp10) REVERT: E 446 ASP cc_start: 0.9263 (m-30) cc_final: 0.8809 (p0) REVERT: E 473 ASP cc_start: 0.8713 (m-30) cc_final: 0.8499 (m-30) REVERT: E 476 LEU cc_start: 0.8748 (mt) cc_final: 0.8226 (mt) REVERT: E 480 LYS cc_start: 0.8975 (mtpt) cc_final: 0.8652 (mtpp) REVERT: E 489 GLN cc_start: 0.8842 (mp10) cc_final: 0.8399 (mp10) REVERT: E 501 PHE cc_start: 0.8914 (t80) cc_final: 0.8473 (t80) REVERT: E 507 GLN cc_start: 0.9413 (tp40) cc_final: 0.9176 (tp-100) REVERT: F 438 GLN cc_start: 0.9120 (mp10) cc_final: 0.8910 (mp10) REVERT: F 441 GLN cc_start: 0.8636 (tp-100) cc_final: 0.8238 (tp40) REVERT: F 482 THR cc_start: 0.8538 (p) cc_final: 0.8105 (p) REVERT: G 445 GLU cc_start: 0.8103 (pm20) cc_final: 0.7389 (pm20) REVERT: G 446 ASP cc_start: 0.8664 (m-30) cc_final: 0.8019 (m-30) REVERT: G 461 ASP cc_start: 0.9157 (m-30) cc_final: 0.8415 (t0) REVERT: G 464 LEU cc_start: 0.9463 (mt) cc_final: 0.9183 (mt) REVERT: G 465 SER cc_start: 0.8554 (m) cc_final: 0.7885 (p) REVERT: G 471 LYS cc_start: 0.7857 (mmpt) cc_final: 0.7518 (mmmm) REVERT: G 475 GLU cc_start: 0.8297 (mp0) cc_final: 0.7564 (tm-30) REVERT: G 485 SER cc_start: 0.8781 (m) cc_final: 0.8239 (p) REVERT: G 488 ARG cc_start: 0.8525 (mmm-85) cc_final: 0.8031 (mmt90) REVERT: G 489 GLN cc_start: 0.8542 (mp10) cc_final: 0.8221 (mp10) REVERT: G 495 ASP cc_start: 0.9041 (m-30) cc_final: 0.8812 (m-30) REVERT: H 451 MET cc_start: 0.9386 (tpp) cc_final: 0.9162 (tpp) REVERT: H 470 MET cc_start: 0.8738 (mpp) cc_final: 0.6831 (mpp) REVERT: H 473 ASP cc_start: 0.9356 (m-30) cc_final: 0.9123 (m-30) REVERT: H 475 GLU cc_start: 0.9475 (mt-10) cc_final: 0.9265 (mt-10) REVERT: H 480 LYS cc_start: 0.8545 (ptpp) cc_final: 0.8070 (ptpp) REVERT: H 488 ARG cc_start: 0.8226 (mmm-85) cc_final: 0.7703 (mmt180) REVERT: H 489 GLN cc_start: 0.8490 (tt0) cc_final: 0.8144 (tt0) REVERT: H 500 GLU cc_start: 0.8504 (mp0) cc_final: 0.8167 (pm20) REVERT: H 501 PHE cc_start: 0.9097 (t80) cc_final: 0.8456 (t80) REVERT: I 474 TYR cc_start: 0.9219 (t80) cc_final: 0.8894 (t80) REVERT: I 475 GLU cc_start: 0.9293 (mt-10) cc_final: 0.8987 (mt-10) REVERT: I 480 LYS cc_start: 0.8998 (mttt) cc_final: 0.8263 (mttt) REVERT: I 486 LYS cc_start: 0.9396 (mtpp) cc_final: 0.9163 (mttm) REVERT: I 492 ASP cc_start: 0.9454 (p0) cc_final: 0.9066 (p0) REVERT: I 495 ASP cc_start: 0.9353 (m-30) cc_final: 0.9069 (m-30) REVERT: I 499 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7781 (mm-30) REVERT: I 515 MET cc_start: 0.5968 (tpt) cc_final: 0.5037 (mmm) REVERT: J 445 GLU cc_start: 0.8770 (mp0) cc_final: 0.8295 (mp0) REVERT: J 449 ASN cc_start: 0.9177 (m-40) cc_final: 0.8790 (m-40) REVERT: J 451 MET cc_start: 0.9238 (tpt) cc_final: 0.8788 (tpp) REVERT: J 453 GLU cc_start: 0.9403 (tp30) cc_final: 0.8843 (tp30) REVERT: J 457 ASN cc_start: 0.8732 (p0) cc_final: 0.8447 (p0) REVERT: J 458 GLN cc_start: 0.9313 (pt0) cc_final: 0.8966 (pt0) REVERT: J 464 LEU cc_start: 0.9390 (tp) cc_final: 0.9120 (tt) REVERT: J 466 ARG cc_start: 0.8965 (mmm-85) cc_final: 0.8745 (mmm-85) REVERT: J 470 MET cc_start: 0.9065 (mtm) cc_final: 0.8785 (mtt) REVERT: J 472 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8118 (mt-10) REVERT: J 489 GLN cc_start: 0.8863 (tm-30) cc_final: 0.8577 (tm-30) REVERT: J 501 PHE cc_start: 0.9138 (t80) cc_final: 0.8647 (t80) REVERT: K 444 ARG cc_start: 0.7276 (ttm170) cc_final: 0.6968 (ptt180) REVERT: K 468 LEU cc_start: 0.9047 (mp) cc_final: 0.7931 (tt) REVERT: K 470 MET cc_start: 0.8220 (mtt) cc_final: 0.7664 (mtt) REVERT: K 471 LYS cc_start: 0.8678 (pttt) cc_final: 0.8465 (pttt) REVERT: K 486 LYS cc_start: 0.9346 (mtpt) cc_final: 0.9121 (mtpp) REVERT: K 489 GLN cc_start: 0.8913 (tm-30) cc_final: 0.8599 (tm-30) REVERT: L 441 GLN cc_start: 0.9133 (tt0) cc_final: 0.8360 (tp-100) REVERT: L 445 GLU cc_start: 0.9003 (pm20) cc_final: 0.8705 (pm20) REVERT: L 446 ASP cc_start: 0.9041 (m-30) cc_final: 0.8758 (m-30) REVERT: L 460 LEU cc_start: 0.9554 (mp) cc_final: 0.9292 (mp) REVERT: L 468 LEU cc_start: 0.9294 (mt) cc_final: 0.8970 (mt) REVERT: L 469 ILE cc_start: 0.8994 (tt) cc_final: 0.8682 (tt) REVERT: L 486 LYS cc_start: 0.9439 (mttp) cc_final: 0.9176 (mtmm) REVERT: L 492 ASP cc_start: 0.9106 (m-30) cc_final: 0.8768 (m-30) REVERT: L 500 GLU cc_start: 0.9336 (mm-30) cc_final: 0.8938 (mm-30) REVERT: L 501 PHE cc_start: 0.9154 (t80) cc_final: 0.8635 (t80) outliers start: 2 outliers final: 0 residues processed: 467 average time/residue: 0.2293 time to fit residues: 139.5287 Evaluate side-chains 415 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 414 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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: 0.8980 chunk 86 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 80 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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** ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN C 489 GLN ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN ** D 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 512 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 449 ASN G 512 ASN ** H 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 449 ASN ** H 458 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 458 GLN K 512 ASN L 512 ASN L 514 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.061831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.049147 restraints weight = 39024.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.051014 restraints weight = 25325.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.052436 restraints weight = 18516.568| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 2.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8328 Z= 0.330 Angle : 0.863 9.216 11184 Z= 0.460 Chirality : 0.047 0.195 1332 Planarity : 0.006 0.102 1440 Dihedral : 5.616 33.912 1092 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: -0.32 (0.17), residues: 852 sheet: None (None), residues: 0 loop : -1.15 (0.51), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A 439 PHE 0.026 0.003 PHE G 501 TYR 0.012 0.002 TYR K 474 ARG 0.009 0.001 ARG A 488 =============================================================================== Job complete usr+sys time: 2985.92 seconds wall clock time: 54 minutes 34.15 seconds (3274.15 seconds total)