Starting phenix.real_space_refine on Tue Sep 24 12:02:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yrn_6842/09_2024/5yrn_6842.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yrn_6842/09_2024/5yrn_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yrn_6842/09_2024/5yrn_6842.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yrn_6842/09_2024/5yrn_6842.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yrn_6842/09_2024/5yrn_6842.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yrn_6842/09_2024/5yrn_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-5461/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: 2.70, per 1000 atoms: 0.33 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: 2.05 Conformation dependent library (CDL) restraints added in 1.1 seconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 87.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 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: 2.04 Time building geometry restraints manager: 2.37 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 19.090 Find NCS groups from input model: 0.300 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.510 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 417 time to evaluate : 0.945 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: 0.3001 time to fit residues: 153.3618 Evaluate side-chains 217 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 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 fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 1.028 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: 0.7940 (ptmm) cc_final: 0.7476 (pmmt) REVERT: A 448 VAL cc_start: 0.8588 (t) cc_final: 0.8189 (p) REVERT: A 492 ASP cc_start: 0.8336 (m-30) cc_final: 0.8007 (m-30) REVERT: A 494 THR cc_start: 0.9296 (m) cc_final: 0.9057 (m) REVERT: A 509 LEU cc_start: 0.9140 (mm) cc_final: 0.8867 (mm) REVERT: B 460 LEU cc_start: 0.7656 (mt) cc_final: 0.7243 (mt) REVERT: B 470 MET cc_start: 0.7854 (mtm) cc_final: 0.7562 (mtt) REVERT: B 503 LYS cc_start: 0.9155 (ttmt) cc_final: 0.8817 (tptt) REVERT: C 479 THR cc_start: 0.6162 (m) cc_final: 0.5670 (m) REVERT: C 480 LYS cc_start: 0.8482 (mppt) cc_final: 0.8238 (mttp) REVERT: C 503 LYS cc_start: 0.8424 (ttmt) cc_final: 0.7922 (tptt) REVERT: C 513 LYS cc_start: 0.8434 (mmmt) cc_final: 0.8075 (tppt) REVERT: D 480 LYS cc_start: 0.8968 (mttp) cc_final: 0.8654 (mtpp) REVERT: D 488 ARG cc_start: 0.8535 (mmm-85) cc_final: 0.8269 (mmm160) REVERT: D 513 LYS cc_start: 0.8591 (pptt) cc_final: 0.8072 (tptp) REVERT: E 461 ASP cc_start: 0.8845 (m-30) cc_final: 0.8370 (t70) REVERT: E 470 MET cc_start: 0.7141 (ptp) cc_final: 0.6760 (ptp) REVERT: E 480 LYS cc_start: 0.8343 (mtpt) cc_final: 0.7998 (ttmt) REVERT: E 483 ARG cc_start: 0.7516 (mtt180) cc_final: 0.7021 (ttm-80) REVERT: G 440 ILE cc_start: 0.9094 (mm) cc_final: 0.8862 (mt) REVERT: G 475 GLU cc_start: 0.7258 (mp0) cc_final: 0.6798 (mt-10) REVERT: H 470 MET cc_start: 0.7467 (mpp) cc_final: 0.7120 (mpp) REVERT: H 471 LYS cc_start: 0.7930 (tttt) cc_final: 0.7685 (pttt) REVERT: H 477 VAL cc_start: 0.6925 (t) cc_final: 0.5425 (p) REVERT: J 435 ILE cc_start: 0.7396 (mt) cc_final: 0.6788 (tp) REVERT: J 443 LYS cc_start: 0.7192 (ptmm) cc_final: 0.6781 (ptmm) REVERT: J 445 GLU cc_start: 0.7434 (mp0) cc_final: 0.6534 (mp0) REVERT: J 446 ASP cc_start: 0.8539 (t0) cc_final: 0.8076 (t0) REVERT: J 499 GLU cc_start: 0.8098 (pp20) cc_final: 0.7773 (tm-30) REVERT: J 501 PHE cc_start: 0.7625 (t80) cc_final: 0.7416 (t80) REVERT: L 430 THR cc_start: 0.8090 (p) cc_final: 0.7759 (t) REVERT: L 453 GLU cc_start: 0.8513 (tm-30) cc_final: 0.7954 (tm-30) REVERT: L 509 LEU cc_start: 0.9143 (tt) cc_final: 0.8834 (pp) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.2604 time to fit residues: 114.2118 Evaluate side-chains 246 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 30.0000 chunk 27 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 30.0000 chunk 87 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 70 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 512 ASN F 437 GLN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 ASN H 512 ASN ** I 437 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 449 ASN J 512 ASN ** J 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN L 497 GLN L 512 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 1.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8328 Z= 0.314 Angle : 0.819 7.884 11184 Z= 0.440 Chirality : 0.046 0.330 1332 Planarity : 0.006 0.062 1440 Dihedral : 5.771 29.423 1092 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.11 % Allowed : 6.22 % Favored : 93.67 % 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: -1.71 (0.23), residues: 1020 helix: -0.91 (0.15), residues: 912 sheet: None (None), residues: 0 loop : -1.35 (0.52), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 439 PHE 0.014 0.003 PHE E 501 TYR 0.013 0.003 TYR D 474 ARG 0.013 0.001 ARG D 488 *********************** 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 468 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 467 time to evaluate : 0.912 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: 0.8352 (ptmm) cc_final: 0.7963 (pmmt) REVERT: A 445 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8207 (mm-30) REVERT: A 461 ASP cc_start: 0.9045 (m-30) cc_final: 0.8633 (m-30) REVERT: A 469 ILE cc_start: 0.9168 (tt) cc_final: 0.8956 (tt) REVERT: A 471 LYS cc_start: 0.9167 (ptpp) cc_final: 0.8826 (ptmm) REVERT: A 476 LEU cc_start: 0.9484 (mt) cc_final: 0.9193 (mt) REVERT: A 480 LYS cc_start: 0.9513 (mmtt) cc_final: 0.9078 (mmmt) REVERT: A 488 ARG cc_start: 0.7789 (mtt-85) cc_final: 0.7511 (mtt-85) REVERT: B 441 GLN cc_start: 0.8452 (mm110) cc_final: 0.8230 (mt0) REVERT: B 443 LYS cc_start: 0.8413 (mtmt) cc_final: 0.8122 (mtpp) REVERT: B 467 ASP cc_start: 0.9348 (t0) cc_final: 0.9116 (t0) REVERT: B 470 MET cc_start: 0.8501 (mtm) cc_final: 0.7908 (mtt) REVERT: B 480 LYS cc_start: 0.8941 (mttp) cc_final: 0.8671 (mmmm) REVERT: B 503 LYS cc_start: 0.9266 (ttmt) cc_final: 0.9003 (tptt) REVERT: C 445 GLU cc_start: 0.8204 (tp30) cc_final: 0.7727 (tp30) REVERT: C 447 ILE cc_start: 0.7904 (mt) cc_final: 0.7537 (mt) REVERT: C 461 ASP cc_start: 0.8413 (m-30) cc_final: 0.7553 (m-30) REVERT: C 470 MET cc_start: 0.8912 (mtp) cc_final: 0.8617 (mtm) REVERT: C 479 THR cc_start: 0.7591 (m) cc_final: 0.6404 (m) REVERT: C 491 LEU cc_start: 0.8082 (mp) cc_final: 0.7540 (tt) REVERT: C 513 LYS cc_start: 0.8570 (mmmt) cc_final: 0.8280 (tppt) REVERT: D 446 ASP cc_start: 0.9098 (m-30) cc_final: 0.8887 (m-30) REVERT: D 477 VAL cc_start: 0.8485 (t) cc_final: 0.8126 (t) REVERT: D 480 LYS cc_start: 0.8860 (mttp) cc_final: 0.8378 (ttmm) REVERT: D 483 ARG cc_start: 0.8466 (mtt180) cc_final: 0.7638 (ttp80) REVERT: D 507 GLN cc_start: 0.9089 (tm-30) cc_final: 0.8699 (tp-100) REVERT: D 513 LYS cc_start: 0.8861 (pptt) cc_final: 0.8655 (mmmt) REVERT: E 437 GLN cc_start: 0.9349 (tt0) cc_final: 0.9088 (tt0) REVERT: E 461 ASP cc_start: 0.8871 (m-30) cc_final: 0.7711 (t70) REVERT: E 470 MET cc_start: 0.7825 (ptp) cc_final: 0.7617 (ptp) REVERT: E 473 ASP cc_start: 0.8248 (m-30) cc_final: 0.7748 (m-30) REVERT: E 474 TYR cc_start: 0.9209 (t80) cc_final: 0.8964 (t80) REVERT: E 480 LYS cc_start: 0.9100 (mtpt) cc_final: 0.8800 (ttmt) REVERT: E 483 ARG cc_start: 0.8148 (mtt180) cc_final: 0.7501 (ttm-80) REVERT: E 503 LYS cc_start: 0.9483 (pttm) cc_final: 0.9184 (pttm) REVERT: E 507 GLN cc_start: 0.9411 (tp-100) cc_final: 0.9211 (tp-100) REVERT: F 450 GLN cc_start: 0.8012 (mt0) cc_final: 0.7672 (mm-40) REVERT: F 460 LEU cc_start: 0.7699 (mt) cc_final: 0.7400 (mt) REVERT: F 461 ASP cc_start: 0.8565 (t70) cc_final: 0.6259 (t0) REVERT: G 449 ASN cc_start: 0.8531 (t0) cc_final: 0.8197 (t0) REVERT: G 475 GLU cc_start: 0.7495 (mp0) cc_final: 0.6791 (pt0) REVERT: G 489 GLN cc_start: 0.8470 (mp10) cc_final: 0.8231 (mp10) REVERT: G 497 GLN cc_start: 0.3094 (mm-40) cc_final: 0.2712 (tt0) REVERT: G 503 LYS cc_start: 0.9455 (pttm) cc_final: 0.9188 (pttp) REVERT: H 441 GLN cc_start: 0.9162 (mt0) cc_final: 0.8957 (pp30) REVERT: H 443 LYS cc_start: 0.8983 (mttt) cc_final: 0.8498 (mtmm) REVERT: H 453 GLU cc_start: 0.9028 (pm20) cc_final: 0.8814 (pm20) REVERT: H 470 MET cc_start: 0.8370 (mpp) cc_final: 0.6316 (mpp) REVERT: H 471 LYS cc_start: 0.8566 (tttt) cc_final: 0.8299 (pttt) REVERT: H 473 ASP cc_start: 0.7631 (m-30) cc_final: 0.6340 (m-30) REVERT: H 485 SER cc_start: 0.9270 (m) cc_final: 0.8799 (p) REVERT: H 489 GLN cc_start: 0.8339 (tt0) cc_final: 0.8113 (tt0) REVERT: I 445 GLU cc_start: 0.8806 (tt0) cc_final: 0.8579 (mm-30) REVERT: I 447 ILE cc_start: 0.8099 (mt) cc_final: 0.7878 (mt) REVERT: I 482 THR cc_start: 0.9017 (p) cc_final: 0.7709 (p) REVERT: I 503 LYS cc_start: 0.8563 (pttp) cc_final: 0.8247 (pttp) REVERT: I 515 MET cc_start: 0.6557 (tpp) cc_final: 0.6137 (tpp) REVERT: J 438 GLN cc_start: 0.8873 (pt0) cc_final: 0.8651 (pp30) REVERT: J 445 GLU cc_start: 0.8006 (mp0) cc_final: 0.7569 (mp0) REVERT: J 449 ASN cc_start: 0.8912 (m110) cc_final: 0.8586 (m-40) REVERT: J 469 ILE cc_start: 0.9362 (tt) cc_final: 0.9157 (tt) REVERT: J 470 MET cc_start: 0.8624 (mtm) cc_final: 0.7950 (mtm) REVERT: J 479 THR cc_start: 0.8392 (t) cc_final: 0.8190 (p) REVERT: J 480 LYS cc_start: 0.9375 (mmtt) cc_final: 0.9172 (mmmt) REVERT: J 486 LYS cc_start: 0.9453 (mtpt) cc_final: 0.9128 (mttt) REVERT: K 444 ARG cc_start: 0.6739 (ttm170) cc_final: 0.6092 (ptt-90) REVERT: K 448 VAL cc_start: 0.9257 (t) cc_final: 0.9013 (m) REVERT: K 453 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8361 (tm-30) REVERT: K 456 LEU cc_start: 0.8297 (tp) cc_final: 0.7949 (tp) REVERT: K 457 ASN cc_start: 0.8460 (t0) cc_final: 0.8050 (t0) REVERT: L 441 GLN cc_start: 0.9118 (mt0) cc_final: 0.8653 (tm-30) REVERT: L 453 GLU cc_start: 0.8547 (tm-30) cc_final: 0.7954 (tm-30) REVERT: L 457 ASN cc_start: 0.8709 (p0) cc_final: 0.8326 (p0) REVERT: L 479 THR cc_start: 0.8729 (t) cc_final: 0.8520 (p) REVERT: L 489 GLN cc_start: 0.9202 (mm110) cc_final: 0.8525 (tt0) REVERT: L 492 ASP cc_start: 0.9342 (m-30) cc_final: 0.8916 (m-30) REVERT: L 496 ILE cc_start: 0.8277 (pt) cc_final: 0.8056 (pt) outliers start: 1 outliers final: 0 residues processed: 467 average time/residue: 0.2503 time to fit residues: 148.4743 Evaluate side-chains 335 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 41 optimal weight: 0.0870 chunk 58 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 GLN ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 512 ASN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 ASN H 441 GLN H 450 GLN ** H 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 458 GLN I 514 GLN J 449 ASN J 497 GLN K 507 GLN K 512 ASN L 514 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 1.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8328 Z= 0.225 Angle : 0.677 9.417 11184 Z= 0.362 Chirality : 0.041 0.151 1332 Planarity : 0.004 0.063 1440 Dihedral : 5.070 19.781 1092 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % 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: -0.37 (0.24), residues: 1020 helix: 0.03 (0.16), residues: 888 sheet: None (None), residues: 0 loop : -1.22 (0.49), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP J 439 PHE 0.021 0.002 PHE G 501 TYR 0.018 0.002 TYR H 474 ARG 0.006 0.001 ARG C 488 *********************** 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 426 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 426 time to evaluate : 0.930 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 446 ASP cc_start: 0.8369 (t0) cc_final: 0.7970 (t0) REVERT: A 470 MET cc_start: 0.8531 (mtt) cc_final: 0.8130 (mtt) REVERT: A 471 LYS cc_start: 0.9103 (ptpp) cc_final: 0.8562 (ptmm) REVERT: A 476 LEU cc_start: 0.9577 (mt) cc_final: 0.9297 (mt) REVERT: A 480 LYS cc_start: 0.9466 (mmtt) cc_final: 0.9239 (mmmt) REVERT: A 500 GLU cc_start: 0.8638 (pm20) cc_final: 0.8112 (pm20) REVERT: A 513 LYS cc_start: 0.9121 (mmpt) cc_final: 0.8891 (mmmt) REVERT: B 458 GLN cc_start: 0.9089 (mp10) cc_final: 0.8842 (mt0) REVERT: B 470 MET cc_start: 0.8221 (mtm) cc_final: 0.7777 (mtt) REVERT: B 503 LYS cc_start: 0.9273 (ttmt) cc_final: 0.8954 (tptt) REVERT: B 515 MET cc_start: 0.6986 (tmm) cc_final: 0.6456 (tmm) REVERT: C 440 ILE cc_start: 0.8655 (mt) cc_final: 0.8378 (mt) REVERT: C 470 MET cc_start: 0.8732 (mtp) cc_final: 0.8265 (mtm) REVERT: C 476 LEU cc_start: 0.9365 (mt) cc_final: 0.9072 (mt) REVERT: C 513 LYS cc_start: 0.8641 (mmmt) cc_final: 0.8370 (tppt) REVERT: D 440 ILE cc_start: 0.9113 (mt) cc_final: 0.8893 (mt) REVERT: D 441 GLN cc_start: 0.8240 (tp-100) cc_final: 0.7700 (tp-100) REVERT: D 461 ASP cc_start: 0.8694 (m-30) cc_final: 0.8332 (m-30) REVERT: D 471 LYS cc_start: 0.9586 (tmtt) cc_final: 0.8605 (tmtt) REVERT: D 474 TYR cc_start: 0.9373 (t80) cc_final: 0.8987 (t80) REVERT: D 475 GLU cc_start: 0.9239 (tp30) cc_final: 0.8825 (pt0) REVERT: D 483 ARG cc_start: 0.8505 (mtt180) cc_final: 0.7805 (ttp80) REVERT: D 488 ARG cc_start: 0.9051 (ptp-110) cc_final: 0.8750 (mtt-85) REVERT: D 503 LYS cc_start: 0.9039 (pttm) cc_final: 0.8777 (pttm) REVERT: D 507 GLN cc_start: 0.9168 (tm-30) cc_final: 0.8765 (tp-100) REVERT: E 438 GLN cc_start: 0.9311 (pp30) cc_final: 0.8984 (pp30) REVERT: E 446 ASP cc_start: 0.9285 (m-30) cc_final: 0.8996 (m-30) REVERT: E 461 ASP cc_start: 0.8092 (m-30) cc_final: 0.7289 (t70) REVERT: E 468 LEU cc_start: 0.9336 (mp) cc_final: 0.9000 (mp) REVERT: E 470 MET cc_start: 0.8274 (ptp) cc_final: 0.7837 (ptp) REVERT: E 471 LYS cc_start: 0.8669 (ttmt) cc_final: 0.8072 (tmtt) REVERT: E 473 ASP cc_start: 0.8553 (m-30) cc_final: 0.8052 (m-30) REVERT: E 474 TYR cc_start: 0.9320 (t80) cc_final: 0.9077 (t80) REVERT: E 480 LYS cc_start: 0.8842 (mtpt) cc_final: 0.8523 (ttmm) REVERT: E 483 ARG cc_start: 0.8465 (mtt180) cc_final: 0.8242 (ttm170) REVERT: E 486 LYS cc_start: 0.8917 (mttm) cc_final: 0.8422 (mtpp) REVERT: E 489 GLN cc_start: 0.8859 (mp10) cc_final: 0.8649 (mm-40) REVERT: F 449 ASN cc_start: 0.8344 (m-40) cc_final: 0.7955 (m-40) REVERT: F 450 GLN cc_start: 0.8196 (mt0) cc_final: 0.7831 (mm-40) REVERT: F 460 LEU cc_start: 0.8094 (mt) cc_final: 0.7845 (mt) REVERT: F 461 ASP cc_start: 0.8656 (t70) cc_final: 0.6806 (t0) REVERT: G 457 ASN cc_start: 0.8924 (m110) cc_final: 0.8626 (p0) REVERT: G 461 ASP cc_start: 0.8670 (m-30) cc_final: 0.8324 (m-30) REVERT: G 475 GLU cc_start: 0.7566 (mp0) cc_final: 0.6698 (pt0) REVERT: G 485 SER cc_start: 0.8274 (m) cc_final: 0.7662 (m) REVERT: G 506 VAL cc_start: 0.9360 (t) cc_final: 0.9108 (t) REVERT: H 443 LYS cc_start: 0.8985 (mttt) cc_final: 0.8536 (mtmm) REVERT: H 470 MET cc_start: 0.8598 (mpp) cc_final: 0.6848 (mpp) REVERT: H 473 ASP cc_start: 0.7679 (m-30) cc_final: 0.6849 (m-30) REVERT: H 485 SER cc_start: 0.9172 (m) cc_final: 0.8801 (p) REVERT: H 489 GLN cc_start: 0.8430 (tt0) cc_final: 0.8216 (tt0) REVERT: H 500 GLU cc_start: 0.7900 (mp0) cc_final: 0.7524 (pm20) REVERT: H 501 PHE cc_start: 0.8544 (t80) cc_final: 0.8215 (t80) REVERT: H 515 MET cc_start: 0.3162 (mmp) cc_final: 0.2159 (tpp) REVERT: I 447 ILE cc_start: 0.8039 (mt) cc_final: 0.7789 (mm) REVERT: I 450 GLN cc_start: 0.8628 (tt0) cc_final: 0.8193 (tt0) REVERT: I 475 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8701 (mt-10) REVERT: I 503 LYS cc_start: 0.8477 (pttp) cc_final: 0.8244 (pttp) REVERT: J 441 GLN cc_start: 0.7484 (tm-30) cc_final: 0.7231 (tm-30) REVERT: J 445 GLU cc_start: 0.8445 (mp0) cc_final: 0.7749 (mp0) REVERT: J 449 ASN cc_start: 0.8843 (m-40) cc_final: 0.8584 (m-40) REVERT: J 470 MET cc_start: 0.8423 (mtm) cc_final: 0.8017 (mtm) REVERT: J 482 THR cc_start: 0.8511 (p) cc_final: 0.7957 (p) REVERT: J 484 THR cc_start: 0.8127 (p) cc_final: 0.7769 (p) REVERT: K 444 ARG cc_start: 0.6557 (ttm170) cc_final: 0.6134 (ptt-90) REVERT: K 453 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8372 (tm-30) REVERT: K 456 LEU cc_start: 0.8704 (tp) cc_final: 0.8385 (tp) REVERT: K 457 ASN cc_start: 0.8459 (t0) cc_final: 0.8192 (t0) REVERT: K 471 LYS cc_start: 0.8022 (mmtm) cc_final: 0.7679 (mmmt) REVERT: K 486 LYS cc_start: 0.8280 (mtpt) cc_final: 0.7197 (mttm) REVERT: L 441 GLN cc_start: 0.9088 (mt0) cc_final: 0.8598 (tm-30) REVERT: L 453 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8077 (tm-30) REVERT: L 457 ASN cc_start: 0.8875 (p0) cc_final: 0.8442 (p0) REVERT: L 476 LEU cc_start: 0.9217 (mt) cc_final: 0.8915 (mt) REVERT: L 486 LYS cc_start: 0.9130 (mttp) cc_final: 0.8862 (mtmm) REVERT: L 489 GLN cc_start: 0.9179 (mm110) cc_final: 0.8397 (tp40) REVERT: L 492 ASP cc_start: 0.9276 (m-30) cc_final: 0.8747 (m-30) outliers start: 0 outliers final: 0 residues processed: 426 average time/residue: 0.2395 time to fit residues: 130.5319 Evaluate side-chains 348 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 348 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 GLN ** E 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 512 ASN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 512 ASN ** I 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 507 GLN K 512 ASN L 497 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 1.5812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8328 Z= 0.230 Angle : 0.695 7.293 11184 Z= 0.376 Chirality : 0.042 0.153 1332 Planarity : 0.004 0.064 1440 Dihedral : 4.939 16.757 1092 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.11 % Allowed : 3.16 % Favored : 96.73 % 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: -0.18 (0.24), residues: 1020 helix: 0.14 (0.17), residues: 852 sheet: None (None), residues: 0 loop : -0.78 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP K 439 PHE 0.014 0.002 PHE H 501 TYR 0.018 0.002 TYR H 474 ARG 0.012 0.001 ARG G 483 *********************** 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 437 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 436 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 ASP cc_start: 0.8939 (m-30) cc_final: 0.8383 (t70) REVERT: A 468 LEU cc_start: 0.9452 (mm) cc_final: 0.9133 (mm) REVERT: A 469 ILE cc_start: 0.9150 (tt) cc_final: 0.8871 (tt) REVERT: A 470 MET cc_start: 0.8698 (mtt) cc_final: 0.8017 (mtt) REVERT: A 472 GLU cc_start: 0.9170 (mp0) cc_final: 0.8833 (mp0) REVERT: A 476 LEU cc_start: 0.9604 (mt) cc_final: 0.9335 (mt) REVERT: A 479 THR cc_start: 0.9023 (t) cc_final: 0.8619 (p) REVERT: A 480 LYS cc_start: 0.9408 (mmtt) cc_final: 0.9080 (mmmt) REVERT: A 488 ARG cc_start: 0.8317 (ttm-80) cc_final: 0.8017 (ttm-80) REVERT: A 492 ASP cc_start: 0.9117 (m-30) cc_final: 0.8845 (m-30) REVERT: A 500 GLU cc_start: 0.8292 (pm20) cc_final: 0.8012 (pm20) REVERT: A 501 PHE cc_start: 0.9066 (t80) cc_final: 0.8642 (t80) REVERT: A 513 LYS cc_start: 0.9082 (mmpt) cc_final: 0.8867 (mmmt) REVERT: B 458 GLN cc_start: 0.9067 (mp10) cc_final: 0.8713 (pt0) REVERT: B 486 LYS cc_start: 0.9184 (mttp) cc_final: 0.8962 (mmtp) REVERT: B 492 ASP cc_start: 0.8659 (m-30) cc_final: 0.8440 (m-30) REVERT: B 500 GLU cc_start: 0.7335 (pm20) cc_final: 0.6955 (pm20) REVERT: B 515 MET cc_start: 0.6883 (tmm) cc_final: 0.6642 (tmm) REVERT: C 440 ILE cc_start: 0.8745 (mt) cc_final: 0.8441 (mt) REVERT: C 461 ASP cc_start: 0.8965 (m-30) cc_final: 0.8461 (m-30) REVERT: C 470 MET cc_start: 0.8789 (mtp) cc_final: 0.8160 (mtm) REVERT: C 476 LEU cc_start: 0.9330 (mt) cc_final: 0.9094 (mt) REVERT: C 491 LEU cc_start: 0.8083 (mp) cc_final: 0.7632 (tt) REVERT: C 513 LYS cc_start: 0.8650 (mmmt) cc_final: 0.8410 (tppt) REVERT: D 461 ASP cc_start: 0.8885 (m-30) cc_final: 0.8665 (t0) REVERT: D 471 LYS cc_start: 0.9535 (tmtt) cc_final: 0.8371 (tmtt) REVERT: D 476 LEU cc_start: 0.9192 (mt) cc_final: 0.8990 (mt) REVERT: D 480 LYS cc_start: 0.9168 (mmtp) cc_final: 0.8726 (mmmm) REVERT: D 483 ARG cc_start: 0.8667 (mtt180) cc_final: 0.8152 (ttp80) REVERT: D 488 ARG cc_start: 0.9102 (ptp-110) cc_final: 0.8867 (ptp-170) REVERT: D 503 LYS cc_start: 0.9005 (pttm) cc_final: 0.8761 (pttm) REVERT: D 507 GLN cc_start: 0.9254 (tm-30) cc_final: 0.8895 (tp-100) REVERT: E 443 LYS cc_start: 0.9333 (ptpt) cc_final: 0.8908 (ptpp) REVERT: E 446 ASP cc_start: 0.9225 (m-30) cc_final: 0.8835 (m-30) REVERT: E 453 GLU cc_start: 0.8749 (tm-30) cc_final: 0.7799 (tp30) REVERT: E 461 ASP cc_start: 0.8251 (m-30) cc_final: 0.7184 (t70) REVERT: E 470 MET cc_start: 0.8460 (ptp) cc_final: 0.7977 (ptp) REVERT: E 471 LYS cc_start: 0.8694 (ttmt) cc_final: 0.8039 (tmtt) REVERT: E 473 ASP cc_start: 0.8875 (m-30) cc_final: 0.8508 (m-30) REVERT: E 474 TYR cc_start: 0.9243 (t80) cc_final: 0.9041 (t80) REVERT: E 480 LYS cc_start: 0.9192 (mtpt) cc_final: 0.8727 (ttmm) REVERT: E 483 ARG cc_start: 0.8715 (mtt180) cc_final: 0.8389 (ttm170) REVERT: E 489 GLN cc_start: 0.8803 (mp10) cc_final: 0.8420 (mp10) REVERT: E 503 LYS cc_start: 0.9384 (pttm) cc_final: 0.9031 (ptpp) REVERT: F 449 ASN cc_start: 0.8345 (m-40) cc_final: 0.7838 (m-40) REVERT: F 450 GLN cc_start: 0.8268 (mt0) cc_final: 0.7725 (mm-40) REVERT: G 446 ASP cc_start: 0.8900 (m-30) cc_final: 0.8235 (m-30) REVERT: G 461 ASP cc_start: 0.8659 (m-30) cc_final: 0.8291 (t0) REVERT: G 475 GLU cc_start: 0.7640 (mp0) cc_final: 0.6992 (tp30) REVERT: G 485 SER cc_start: 0.8382 (m) cc_final: 0.7785 (m) REVERT: G 509 LEU cc_start: 0.9017 (tt) cc_final: 0.8602 (pp) REVERT: H 441 GLN cc_start: 0.8761 (pp30) cc_final: 0.8469 (pp30) REVERT: H 470 MET cc_start: 0.8789 (mpp) cc_final: 0.6402 (mpp) REVERT: H 471 LYS cc_start: 0.8197 (pttt) cc_final: 0.7995 (pttt) REVERT: H 473 ASP cc_start: 0.7802 (m-30) cc_final: 0.6780 (m-30) REVERT: H 480 LYS cc_start: 0.8643 (mtmt) cc_final: 0.7712 (ptpt) REVERT: H 485 SER cc_start: 0.9195 (m) cc_final: 0.7390 (p) REVERT: H 486 LYS cc_start: 0.8888 (mtpp) cc_final: 0.7997 (mttm) REVERT: H 495 ASP cc_start: 0.9480 (m-30) cc_final: 0.9181 (m-30) REVERT: I 447 ILE cc_start: 0.8163 (mt) cc_final: 0.7934 (mt) REVERT: I 450 GLN cc_start: 0.8629 (tt0) cc_final: 0.8195 (tt0) REVERT: I 461 ASP cc_start: 0.8630 (t70) cc_final: 0.8233 (t70) REVERT: I 468 LEU cc_start: 0.8488 (tp) cc_final: 0.8287 (tp) REVERT: I 475 GLU cc_start: 0.9342 (mm-30) cc_final: 0.9040 (mt-10) REVERT: I 476 LEU cc_start: 0.9449 (mt) cc_final: 0.9191 (mt) REVERT: I 479 THR cc_start: 0.8719 (m) cc_final: 0.8375 (p) REVERT: I 480 LYS cc_start: 0.8906 (mmtm) cc_final: 0.8532 (mtmp) REVERT: I 515 MET cc_start: 0.6069 (tpt) cc_final: 0.5804 (tpt) REVERT: J 445 GLU cc_start: 0.8581 (mp0) cc_final: 0.8266 (mp0) REVERT: J 457 ASN cc_start: 0.8854 (p0) cc_final: 0.8649 (p0) REVERT: J 458 GLN cc_start: 0.9253 (tm-30) cc_final: 0.9006 (tm-30) REVERT: J 467 ASP cc_start: 0.9118 (p0) cc_final: 0.8529 (p0) REVERT: J 469 ILE cc_start: 0.9299 (tt) cc_final: 0.8952 (tt) REVERT: J 470 MET cc_start: 0.9108 (mtm) cc_final: 0.8424 (mtt) REVERT: J 476 LEU cc_start: 0.9569 (mt) cc_final: 0.9356 (mt) REVERT: J 487 VAL cc_start: 0.9396 (t) cc_final: 0.9163 (p) REVERT: K 444 ARG cc_start: 0.6547 (ttm170) cc_final: 0.6073 (ptt180) REVERT: K 456 LEU cc_start: 0.9316 (tp) cc_final: 0.9001 (tp) REVERT: K 460 LEU cc_start: 0.9294 (mt) cc_final: 0.9089 (mt) REVERT: K 471 LYS cc_start: 0.8430 (mmtm) cc_final: 0.8191 (mmmt) REVERT: K 480 LYS cc_start: 0.6638 (mtmt) cc_final: 0.5993 (mtmt) REVERT: K 485 SER cc_start: 0.9296 (m) cc_final: 0.9013 (p) REVERT: L 441 GLN cc_start: 0.9235 (mt0) cc_final: 0.8580 (tm-30) REVERT: L 453 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8378 (tm-30) REVERT: L 469 ILE cc_start: 0.8722 (tt) cc_final: 0.8517 (tt) REVERT: L 472 GLU cc_start: 0.7969 (tt0) cc_final: 0.7673 (tt0) REVERT: L 476 LEU cc_start: 0.9295 (mt) cc_final: 0.9032 (mt) REVERT: L 480 LYS cc_start: 0.9481 (mmtm) cc_final: 0.9245 (mmmm) REVERT: L 486 LYS cc_start: 0.9205 (mttp) cc_final: 0.8952 (mtmm) REVERT: L 489 GLN cc_start: 0.9251 (mm110) cc_final: 0.8817 (tp40) REVERT: L 492 ASP cc_start: 0.9293 (m-30) cc_final: 0.8770 (m-30) outliers start: 1 outliers final: 0 residues processed: 436 average time/residue: 0.2323 time to fit residues: 130.3543 Evaluate side-chains 358 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 GLN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 457 ASN E 458 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 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 ASN ** H 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 512 ASN I 437 GLN K 512 ASN K 514 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 1.6599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8328 Z= 0.214 Angle : 0.678 6.889 11184 Z= 0.366 Chirality : 0.042 0.161 1332 Planarity : 0.004 0.064 1440 Dihedral : 4.851 21.276 1092 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.11 % Allowed : 2.53 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.13 (0.25), residues: 1020 helix: 0.35 (0.17), residues: 852 sheet: None (None), residues: 0 loop : -0.67 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 439 PHE 0.016 0.002 PHE H 501 TYR 0.017 0.002 TYR H 474 ARG 0.004 0.001 ARG D 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 442 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 441 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 ASP cc_start: 0.9030 (m-30) cc_final: 0.8730 (m-30) REVERT: A 470 MET cc_start: 0.8807 (mtt) cc_final: 0.8084 (mtt) REVERT: A 472 GLU cc_start: 0.9133 (mp0) cc_final: 0.8814 (mp0) REVERT: A 479 THR cc_start: 0.8950 (t) cc_final: 0.8724 (p) REVERT: A 492 ASP cc_start: 0.9144 (m-30) cc_final: 0.8891 (m-30) REVERT: B 458 GLN cc_start: 0.9005 (mp10) cc_final: 0.8739 (pt0) REVERT: B 500 GLU cc_start: 0.7565 (pm20) cc_final: 0.7134 (pm20) REVERT: C 440 ILE cc_start: 0.8867 (mt) cc_final: 0.8597 (mt) REVERT: C 461 ASP cc_start: 0.8939 (m-30) cc_final: 0.8610 (m-30) REVERT: C 475 GLU cc_start: 0.8513 (pp20) cc_final: 0.6693 (pp20) REVERT: C 476 LEU cc_start: 0.9472 (mt) cc_final: 0.9211 (mt) REVERT: C 491 LEU cc_start: 0.8619 (mp) cc_final: 0.8069 (tt) REVERT: C 492 ASP cc_start: 0.9268 (m-30) cc_final: 0.8934 (m-30) REVERT: D 458 GLN cc_start: 0.8741 (mp10) cc_final: 0.8395 (pt0) REVERT: D 461 ASP cc_start: 0.8930 (m-30) cc_final: 0.8549 (t70) REVERT: D 469 ILE cc_start: 0.8913 (tt) cc_final: 0.8598 (tt) REVERT: D 472 GLU cc_start: 0.8706 (tt0) cc_final: 0.7823 (tt0) REVERT: D 474 TYR cc_start: 0.9394 (t80) cc_final: 0.8737 (t80) REVERT: D 476 LEU cc_start: 0.9194 (mt) cc_final: 0.8955 (mt) REVERT: D 479 THR cc_start: 0.8667 (m) cc_final: 0.8399 (p) REVERT: D 480 LYS cc_start: 0.9217 (mmtp) cc_final: 0.8671 (mmmm) REVERT: D 483 ARG cc_start: 0.8781 (mtt180) cc_final: 0.8472 (ttp80) REVERT: E 438 GLN cc_start: 0.9294 (pp30) cc_final: 0.9060 (pp30) REVERT: E 446 ASP cc_start: 0.9169 (m-30) cc_final: 0.8916 (m-30) REVERT: E 453 GLU cc_start: 0.8856 (tm-30) cc_final: 0.7868 (tp30) REVERT: E 461 ASP cc_start: 0.8195 (m-30) cc_final: 0.7125 (t70) REVERT: E 470 MET cc_start: 0.8593 (ptp) cc_final: 0.8120 (ptp) REVERT: E 471 LYS cc_start: 0.8712 (ttmt) cc_final: 0.8431 (tmtt) REVERT: E 473 ASP cc_start: 0.8953 (m-30) cc_final: 0.8698 (m-30) REVERT: E 483 ARG cc_start: 0.8795 (mtt180) cc_final: 0.8527 (ttm170) REVERT: E 486 LYS cc_start: 0.9207 (mttm) cc_final: 0.8827 (mmmm) REVERT: E 489 GLN cc_start: 0.8844 (mp10) cc_final: 0.8626 (mp10) REVERT: E 494 THR cc_start: 0.9483 (m) cc_final: 0.9083 (m) REVERT: E 501 PHE cc_start: 0.8828 (t80) cc_final: 0.8016 (t80) REVERT: E 503 LYS cc_start: 0.9421 (pttm) cc_final: 0.9058 (pttm) REVERT: F 449 ASN cc_start: 0.8444 (m-40) cc_final: 0.8037 (m-40) REVERT: F 450 GLN cc_start: 0.8343 (mt0) cc_final: 0.7788 (mm-40) REVERT: G 442 SER cc_start: 0.8641 (t) cc_final: 0.8351 (p) REVERT: G 446 ASP cc_start: 0.8862 (m-30) cc_final: 0.8175 (m-30) REVERT: G 461 ASP cc_start: 0.8808 (m-30) cc_final: 0.8299 (t0) REVERT: G 470 MET cc_start: -0.1516 (ptt) cc_final: -0.1793 (ptt) REVERT: G 475 GLU cc_start: 0.7700 (mp0) cc_final: 0.6582 (tm-30) REVERT: G 485 SER cc_start: 0.8403 (m) cc_final: 0.7927 (m) REVERT: G 503 LYS cc_start: 0.9436 (ptpp) cc_final: 0.9084 (pttp) REVERT: H 446 ASP cc_start: 0.8972 (m-30) cc_final: 0.8623 (m-30) REVERT: H 470 MET cc_start: 0.8894 (mpp) cc_final: 0.6847 (mpp) REVERT: H 473 ASP cc_start: 0.8111 (m-30) cc_final: 0.7253 (m-30) REVERT: H 485 SER cc_start: 0.9045 (m) cc_final: 0.7877 (p) REVERT: H 486 LYS cc_start: 0.8917 (mtpp) cc_final: 0.7796 (mttm) REVERT: H 500 GLU cc_start: 0.7977 (mp0) cc_final: 0.7712 (pm20) REVERT: H 515 MET cc_start: 0.4173 (mmp) cc_final: 0.3238 (tpp) REVERT: I 450 GLN cc_start: 0.8616 (tt0) cc_final: 0.8208 (tt0) REVERT: I 461 ASP cc_start: 0.8856 (t70) cc_final: 0.8611 (t70) REVERT: I 475 GLU cc_start: 0.9402 (mm-30) cc_final: 0.9105 (mt-10) REVERT: I 476 LEU cc_start: 0.9522 (mt) cc_final: 0.9290 (mt) REVERT: I 479 THR cc_start: 0.8747 (m) cc_final: 0.8409 (p) REVERT: I 480 LYS cc_start: 0.8877 (mmtm) cc_final: 0.8637 (mttt) REVERT: I 515 MET cc_start: 0.6205 (tpt) cc_final: 0.5782 (tpp) REVERT: J 445 GLU cc_start: 0.8672 (mp0) cc_final: 0.8284 (mp0) REVERT: J 446 ASP cc_start: 0.8926 (p0) cc_final: 0.8678 (p0) REVERT: J 449 ASN cc_start: 0.8888 (m-40) cc_final: 0.8631 (m-40) REVERT: J 467 ASP cc_start: 0.9108 (p0) cc_final: 0.8192 (p0) REVERT: J 470 MET cc_start: 0.8822 (mtm) cc_final: 0.7736 (mtt) REVERT: J 472 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8467 (mt-10) REVERT: J 476 LEU cc_start: 0.9665 (mt) cc_final: 0.9390 (mt) REVERT: J 489 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8592 (tm-30) REVERT: J 495 ASP cc_start: 0.9522 (m-30) cc_final: 0.9250 (m-30) REVERT: K 444 ARG cc_start: 0.6742 (ttm170) cc_final: 0.5973 (ptt180) REVERT: K 456 LEU cc_start: 0.9382 (tp) cc_final: 0.9151 (tp) REVERT: K 471 LYS cc_start: 0.8609 (mmtm) cc_final: 0.8370 (mmmt) REVERT: K 476 LEU cc_start: 0.9201 (mt) cc_final: 0.8987 (mt) REVERT: K 486 LYS cc_start: 0.8783 (mtpt) cc_final: 0.8500 (mtpp) REVERT: L 441 GLN cc_start: 0.9233 (mt0) cc_final: 0.8853 (tt0) REVERT: L 453 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8449 (tm-30) REVERT: L 472 GLU cc_start: 0.8053 (tt0) cc_final: 0.7775 (tt0) REVERT: L 476 LEU cc_start: 0.9325 (mt) cc_final: 0.9063 (mt) REVERT: L 480 LYS cc_start: 0.9466 (mmtm) cc_final: 0.9249 (mmmm) REVERT: L 486 LYS cc_start: 0.9227 (mttp) cc_final: 0.9013 (mtmm) REVERT: L 489 GLN cc_start: 0.9285 (mm110) cc_final: 0.9067 (mm-40) REVERT: L 492 ASP cc_start: 0.9248 (m-30) cc_final: 0.8783 (m-30) REVERT: L 501 PHE cc_start: 0.8784 (t80) cc_final: 0.8506 (t80) outliers start: 1 outliers final: 0 residues processed: 442 average time/residue: 0.2347 time to fit residues: 133.9023 Evaluate side-chains 368 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.6980 chunk 52 optimal weight: 0.4980 chunk 67 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 57 optimal weight: 0.0270 chunk 56 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 overall best weight: 2.0442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 GLN ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN D 441 GLN D 457 ASN E 507 GLN E 512 ASN F 441 GLN 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 H 514 GLN J 512 ASN K 437 GLN K 512 ASN L 458 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 1.7582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8328 Z= 0.237 Angle : 0.732 7.695 11184 Z= 0.390 Chirality : 0.042 0.143 1332 Planarity : 0.004 0.061 1440 Dihedral : 5.052 20.279 1092 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.14 (0.25), residues: 1020 helix: 0.20 (0.17), residues: 852 sheet: None (None), residues: 0 loop : -0.93 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 439 PHE 0.018 0.002 PHE H 501 TYR 0.015 0.002 TYR G 474 ARG 0.006 0.001 ARG C 488 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 444 time to evaluate : 1.016 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 445 GLU cc_start: 0.8629 (pm20) cc_final: 0.8269 (pm20) REVERT: A 461 ASP cc_start: 0.9081 (m-30) cc_final: 0.8455 (t70) REVERT: A 472 GLU cc_start: 0.9068 (mp0) cc_final: 0.8833 (mp0) REVERT: A 488 ARG cc_start: 0.8494 (ttm-80) cc_final: 0.8114 (ttm-80) REVERT: A 492 ASP cc_start: 0.9288 (m-30) cc_final: 0.9005 (m-30) REVERT: B 458 GLN cc_start: 0.9068 (mp10) cc_final: 0.8842 (pt0) REVERT: B 470 MET cc_start: 0.8480 (mtt) cc_final: 0.8213 (mtp) REVERT: B 472 GLU cc_start: 0.8629 (pm20) cc_final: 0.8035 (pt0) REVERT: B 476 LEU cc_start: 0.9562 (mt) cc_final: 0.9273 (mt) REVERT: B 480 LYS cc_start: 0.8972 (mmmm) cc_final: 0.8720 (mmmm) REVERT: B 492 ASP cc_start: 0.9044 (m-30) cc_final: 0.8841 (m-30) REVERT: B 500 GLU cc_start: 0.7439 (pm20) cc_final: 0.7146 (pm20) REVERT: C 461 ASP cc_start: 0.8970 (m-30) cc_final: 0.8504 (m-30) REVERT: C 470 MET cc_start: 0.8591 (mtm) cc_final: 0.8310 (mtm) REVERT: C 475 GLU cc_start: 0.8585 (pp20) cc_final: 0.8384 (pp20) REVERT: C 489 GLN cc_start: 0.8377 (mp10) cc_final: 0.7936 (mp10) REVERT: C 507 GLN cc_start: 0.9236 (pp30) cc_final: 0.8597 (pp30) REVERT: D 446 ASP cc_start: 0.8799 (m-30) cc_final: 0.8592 (p0) REVERT: D 458 GLN cc_start: 0.8833 (mp10) cc_final: 0.8235 (pt0) REVERT: D 461 ASP cc_start: 0.9097 (m-30) cc_final: 0.8428 (t70) REVERT: D 466 ARG cc_start: 0.8877 (mpp80) cc_final: 0.8632 (mpp80) REVERT: D 472 GLU cc_start: 0.8268 (tt0) cc_final: 0.7782 (tt0) REVERT: D 474 TYR cc_start: 0.9451 (t80) cc_final: 0.9106 (t80) REVERT: D 480 LYS cc_start: 0.9230 (mmtp) cc_final: 0.8701 (mmmm) REVERT: E 446 ASP cc_start: 0.9152 (m-30) cc_final: 0.8819 (m-30) REVERT: E 461 ASP cc_start: 0.8458 (m-30) cc_final: 0.7123 (t70) REVERT: E 470 MET cc_start: 0.8678 (ptp) cc_final: 0.8266 (ptp) REVERT: E 471 LYS cc_start: 0.9066 (ttmt) cc_final: 0.8772 (tmtt) REVERT: E 473 ASP cc_start: 0.9099 (m-30) cc_final: 0.8783 (m-30) REVERT: E 474 TYR cc_start: 0.9317 (t80) cc_final: 0.8971 (t80) REVERT: E 480 LYS cc_start: 0.9146 (mtpt) cc_final: 0.8610 (mtpp) REVERT: E 486 LYS cc_start: 0.9299 (mttm) cc_final: 0.8884 (mmmm) REVERT: E 489 GLN cc_start: 0.8969 (mp10) cc_final: 0.8608 (mp10) REVERT: E 503 LYS cc_start: 0.9447 (pttm) cc_final: 0.9074 (pttm) REVERT: F 447 ILE cc_start: 0.9284 (tp) cc_final: 0.8819 (pt) REVERT: F 449 ASN cc_start: 0.8552 (m-40) cc_final: 0.8161 (m-40) REVERT: F 450 GLN cc_start: 0.8494 (mt0) cc_final: 0.7922 (mm-40) REVERT: F 482 THR cc_start: 0.8522 (t) cc_final: 0.8257 (p) REVERT: G 446 ASP cc_start: 0.8920 (m-30) cc_final: 0.8239 (m-30) REVERT: G 451 MET cc_start: 0.8706 (tpt) cc_final: 0.8474 (tpp) REVERT: G 475 GLU cc_start: 0.7960 (mp0) cc_final: 0.6877 (tm-30) REVERT: G 480 LYS cc_start: 0.8517 (ttmm) cc_final: 0.8314 (ttmm) REVERT: G 485 SER cc_start: 0.8602 (m) cc_final: 0.8327 (m) REVERT: G 503 LYS cc_start: 0.9321 (ptpp) cc_final: 0.9020 (pttp) REVERT: H 470 MET cc_start: 0.9067 (mpp) cc_final: 0.7166 (mpp) REVERT: H 472 GLU cc_start: 0.8943 (pt0) cc_final: 0.8499 (pt0) REVERT: H 473 ASP cc_start: 0.8631 (m-30) cc_final: 0.7786 (m-30) REVERT: H 486 LYS cc_start: 0.8992 (mtpp) cc_final: 0.8373 (mttm) REVERT: H 500 GLU cc_start: 0.8105 (mp0) cc_final: 0.7821 (pm20) REVERT: H 515 MET cc_start: 0.4202 (mmp) cc_final: 0.3870 (mmp) REVERT: I 450 GLN cc_start: 0.8513 (tt0) cc_final: 0.8102 (tt0) REVERT: I 468 LEU cc_start: 0.9147 (tp) cc_final: 0.8836 (tp) REVERT: I 478 SER cc_start: 0.9635 (t) cc_final: 0.9429 (p) REVERT: I 479 THR cc_start: 0.8926 (m) cc_final: 0.8686 (p) REVERT: I 480 LYS cc_start: 0.9041 (mmtm) cc_final: 0.8761 (mttt) REVERT: I 484 THR cc_start: 0.9422 (m) cc_final: 0.9161 (p) REVERT: I 486 LYS cc_start: 0.9158 (mtpp) cc_final: 0.8665 (mttm) REVERT: I 488 ARG cc_start: 0.8869 (ptp-110) cc_final: 0.8636 (ptp90) REVERT: I 515 MET cc_start: 0.6291 (tpt) cc_final: 0.6050 (tpp) REVERT: J 451 MET cc_start: 0.9041 (tpp) cc_final: 0.8781 (tpp) REVERT: J 467 ASP cc_start: 0.8861 (p0) cc_final: 0.8067 (p0) REVERT: J 469 ILE cc_start: 0.8548 (tt) cc_final: 0.8345 (tt) REVERT: J 472 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8057 (mt-10) REVERT: J 476 LEU cc_start: 0.9649 (mt) cc_final: 0.9344 (mt) REVERT: J 495 ASP cc_start: 0.9516 (m-30) cc_final: 0.9257 (m-30) REVERT: K 444 ARG cc_start: 0.6744 (ttm170) cc_final: 0.5969 (ptt180) REVERT: K 456 LEU cc_start: 0.9545 (tp) cc_final: 0.9245 (tp) REVERT: K 469 ILE cc_start: 0.8793 (tt) cc_final: 0.8525 (tt) REVERT: K 470 MET cc_start: 0.2810 (ptt) cc_final: 0.2460 (mtt) REVERT: K 471 LYS cc_start: 0.8862 (mmtm) cc_final: 0.8602 (mmmm) REVERT: K 476 LEU cc_start: 0.9217 (mt) cc_final: 0.9014 (mt) REVERT: K 480 LYS cc_start: 0.7577 (mtmt) cc_final: 0.7296 (mttt) REVERT: K 501 PHE cc_start: 0.6161 (m-80) cc_final: 0.5788 (m-80) REVERT: L 441 GLN cc_start: 0.9263 (mt0) cc_final: 0.8879 (tm-30) REVERT: L 469 ILE cc_start: 0.8862 (tt) cc_final: 0.8617 (tt) REVERT: L 472 GLU cc_start: 0.8025 (tt0) cc_final: 0.7798 (tt0) REVERT: L 476 LEU cc_start: 0.9406 (mt) cc_final: 0.9164 (mt) REVERT: L 480 LYS cc_start: 0.9496 (mmtm) cc_final: 0.9259 (mmmm) REVERT: L 486 LYS cc_start: 0.9244 (mttp) cc_final: 0.8917 (mtmm) REVERT: L 492 ASP cc_start: 0.9251 (m-30) cc_final: 0.8748 (m-30) REVERT: L 500 GLU cc_start: 0.9224 (tp30) cc_final: 0.8883 (mm-30) REVERT: L 501 PHE cc_start: 0.8907 (t80) cc_final: 0.8341 (t80) REVERT: L 503 LYS cc_start: 0.9443 (mtpp) cc_final: 0.9243 (mtpp) outliers start: 0 outliers final: 0 residues processed: 444 average time/residue: 0.2277 time to fit residues: 131.1806 Evaluate side-chains 377 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 377 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 chunk 88 optimal weight: 20.0000 chunk 80 optimal weight: 20.0000 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN D 457 ASN ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 512 ASN I 438 GLN I 489 GLN J 512 ASN K 512 ASN L 514 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 1.8786 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= 0.277 Angle : 0.766 9.242 11184 Z= 0.407 Chirality : 0.044 0.162 1332 Planarity : 0.005 0.065 1440 Dihedral : 5.109 19.299 1092 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.39 (0.25), residues: 1020 helix: 0.02 (0.17), residues: 852 sheet: None (None), residues: 0 loop : -1.02 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 439 PHE 0.017 0.003 PHE G 501 TYR 0.019 0.002 TYR G 474 ARG 0.009 0.001 ARG E 483 *********************** 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 fitting. rotamer outliers: 0 poor density : 466 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 ASP cc_start: 0.8603 (t0) cc_final: 0.8359 (t0) REVERT: A 458 GLN cc_start: 0.9244 (pt0) cc_final: 0.9036 (pt0) REVERT: A 461 ASP cc_start: 0.9065 (m-30) cc_final: 0.8720 (t70) REVERT: A 470 MET cc_start: 0.8953 (mtt) cc_final: 0.8476 (mtt) REVERT: A 480 LYS cc_start: 0.9269 (mmmt) cc_final: 0.9037 (mmmt) REVERT: A 488 ARG cc_start: 0.8471 (ttm-80) cc_final: 0.8127 (ttm-80) REVERT: A 492 ASP cc_start: 0.9090 (m-30) cc_final: 0.8789 (m-30) REVERT: A 500 GLU cc_start: 0.8551 (pm20) cc_final: 0.7904 (pm20) REVERT: B 441 GLN cc_start: 0.8508 (mp10) cc_final: 0.8165 (mp10) REVERT: B 472 GLU cc_start: 0.8548 (pm20) cc_final: 0.7815 (pt0) REVERT: B 476 LEU cc_start: 0.9578 (mt) cc_final: 0.9252 (mt) REVERT: B 479 THR cc_start: 0.8946 (t) cc_final: 0.8500 (p) REVERT: B 480 LYS cc_start: 0.9137 (mmmm) cc_final: 0.8782 (mmmm) REVERT: B 492 ASP cc_start: 0.9160 (m-30) cc_final: 0.8870 (m-30) REVERT: C 461 ASP cc_start: 0.8948 (m-30) cc_final: 0.8456 (m-30) REVERT: C 468 LEU cc_start: 0.9258 (mp) cc_final: 0.8980 (mt) REVERT: C 470 MET cc_start: 0.8587 (mtm) cc_final: 0.8113 (mtm) REVERT: C 472 GLU cc_start: 0.8504 (tt0) cc_final: 0.7708 (tt0) REVERT: C 473 ASP cc_start: 0.9544 (m-30) cc_final: 0.9211 (m-30) REVERT: C 489 GLN cc_start: 0.8451 (mp10) cc_final: 0.8217 (mp10) REVERT: D 441 GLN cc_start: 0.8523 (tp-100) cc_final: 0.8181 (tm-30) REVERT: D 461 ASP cc_start: 0.8949 (m-30) cc_final: 0.8716 (t70) REVERT: D 466 ARG cc_start: 0.8917 (mpp80) cc_final: 0.8580 (mpp80) REVERT: D 470 MET cc_start: 0.8502 (ptt) cc_final: 0.8257 (ppp) REVERT: D 474 TYR cc_start: 0.9465 (t80) cc_final: 0.9050 (t80) REVERT: D 476 LEU cc_start: 0.9309 (mt) cc_final: 0.9081 (mt) REVERT: D 480 LYS cc_start: 0.9177 (mmtp) cc_final: 0.8869 (mmmm) REVERT: D 491 LEU cc_start: 0.9413 (mt) cc_final: 0.9184 (mt) REVERT: E 461 ASP cc_start: 0.8481 (m-30) cc_final: 0.7349 (t70) REVERT: E 470 MET cc_start: 0.8679 (ptp) cc_final: 0.8097 (ptp) REVERT: E 471 LYS cc_start: 0.9069 (ttmt) cc_final: 0.8868 (tmtt) REVERT: E 473 ASP cc_start: 0.9127 (m-30) cc_final: 0.8906 (m-30) REVERT: E 474 TYR cc_start: 0.9312 (t80) cc_final: 0.9054 (t80) REVERT: E 480 LYS cc_start: 0.9165 (mtpt) cc_final: 0.8905 (mtpp) REVERT: E 495 ASP cc_start: 0.9279 (m-30) cc_final: 0.9065 (m-30) REVERT: E 501 PHE cc_start: 0.8825 (t80) cc_final: 0.8160 (t80) REVERT: E 503 LYS cc_start: 0.9453 (pttm) cc_final: 0.9095 (pttm) REVERT: F 447 ILE cc_start: 0.9259 (tp) cc_final: 0.8848 (pt) REVERT: F 450 GLN cc_start: 0.8426 (mt0) cc_final: 0.8013 (mm-40) REVERT: F 460 LEU cc_start: 0.9264 (pp) cc_final: 0.8950 (pp) REVERT: F 461 ASP cc_start: 0.9174 (t70) cc_final: 0.8962 (m-30) REVERT: G 446 ASP cc_start: 0.8960 (m-30) cc_final: 0.8201 (m-30) REVERT: G 461 ASP cc_start: 0.9150 (m-30) cc_final: 0.8273 (t0) REVERT: G 475 GLU cc_start: 0.7686 (mp0) cc_final: 0.6774 (tm-30) REVERT: G 480 LYS cc_start: 0.8623 (ttmm) cc_final: 0.8309 (ttmm) REVERT: G 485 SER cc_start: 0.8508 (m) cc_final: 0.7999 (m) REVERT: G 500 GLU cc_start: 0.8402 (mp0) cc_final: 0.8142 (pm20) REVERT: G 503 LYS cc_start: 0.9224 (ptpp) cc_final: 0.8934 (pttp) REVERT: H 470 MET cc_start: 0.8816 (mpp) cc_final: 0.6894 (mpp) REVERT: H 472 GLU cc_start: 0.9013 (pt0) cc_final: 0.8580 (pt0) REVERT: H 473 ASP cc_start: 0.8940 (m-30) cc_final: 0.8095 (m-30) REVERT: H 480 LYS cc_start: 0.7629 (pttm) cc_final: 0.7238 (pttm) REVERT: H 485 SER cc_start: 0.9226 (m) cc_final: 0.8573 (p) REVERT: H 500 GLU cc_start: 0.8425 (mp0) cc_final: 0.7992 (pm20) REVERT: H 504 VAL cc_start: 0.9291 (t) cc_final: 0.9066 (m) REVERT: H 515 MET cc_start: 0.4563 (mmp) cc_final: 0.4226 (mmp) REVERT: I 450 GLN cc_start: 0.8598 (tt0) cc_final: 0.8145 (tt0) REVERT: I 453 GLU cc_start: 0.9282 (tm-30) cc_final: 0.9018 (tm-30) REVERT: I 463 LEU cc_start: 0.9362 (mt) cc_final: 0.9106 (mt) REVERT: I 478 SER cc_start: 0.9601 (t) cc_final: 0.9377 (p) REVERT: I 480 LYS cc_start: 0.8960 (mmtm) cc_final: 0.8724 (mttt) REVERT: I 484 THR cc_start: 0.9433 (m) cc_final: 0.8753 (p) REVERT: I 486 LYS cc_start: 0.9275 (mtpp) cc_final: 0.9057 (mttm) REVERT: I 488 ARG cc_start: 0.8872 (ptp-110) cc_final: 0.8472 (ptp90) REVERT: I 515 MET cc_start: 0.6434 (tpt) cc_final: 0.6032 (tpp) REVERT: J 449 ASN cc_start: 0.8961 (m-40) cc_final: 0.8755 (m-40) REVERT: J 451 MET cc_start: 0.9169 (tpp) cc_final: 0.8830 (tpp) REVERT: J 467 ASP cc_start: 0.8919 (p0) cc_final: 0.8171 (p0) REVERT: J 470 MET cc_start: 0.8701 (mtt) cc_final: 0.8253 (mtt) REVERT: J 482 THR cc_start: 0.8700 (p) cc_final: 0.8494 (p) REVERT: J 495 ASP cc_start: 0.9464 (m-30) cc_final: 0.9210 (m-30) REVERT: J 499 GLU cc_start: 0.8716 (pm20) cc_final: 0.8387 (tp30) REVERT: J 501 PHE cc_start: 0.9022 (t80) cc_final: 0.8238 (t80) REVERT: K 444 ARG cc_start: 0.7295 (ttm170) cc_final: 0.6386 (ptt180) REVERT: K 456 LEU cc_start: 0.9644 (tp) cc_final: 0.9421 (tp) REVERT: K 471 LYS cc_start: 0.9195 (mmtm) cc_final: 0.8692 (ttpt) REVERT: K 476 LEU cc_start: 0.9428 (mt) cc_final: 0.9163 (mt) REVERT: K 480 LYS cc_start: 0.7492 (mtmt) cc_final: 0.7033 (mtpt) REVERT: K 503 LYS cc_start: 0.9155 (ptmm) cc_final: 0.8689 (ptmm) REVERT: K 504 VAL cc_start: 0.9027 (t) cc_final: 0.8738 (m) REVERT: K 510 LYS cc_start: 0.9030 (pptt) cc_final: 0.8811 (tppt) REVERT: L 441 GLN cc_start: 0.9139 (mt0) cc_final: 0.8931 (tt0) REVERT: L 466 ARG cc_start: 0.8646 (mmm-85) cc_final: 0.8409 (mmm-85) REVERT: L 469 ILE cc_start: 0.8843 (tt) cc_final: 0.8576 (tt) REVERT: L 471 LYS cc_start: 0.8465 (tttt) cc_final: 0.8219 (tttt) REVERT: L 476 LEU cc_start: 0.9434 (mt) cc_final: 0.9216 (mt) REVERT: L 480 LYS cc_start: 0.9494 (mmtm) cc_final: 0.9247 (mmmm) REVERT: L 486 LYS cc_start: 0.9244 (mttp) cc_final: 0.8928 (mtmm) REVERT: L 492 ASP cc_start: 0.9265 (m-30) cc_final: 0.8984 (m-30) REVERT: L 501 PHE cc_start: 0.9067 (t80) cc_final: 0.8786 (t80) outliers start: 0 outliers final: 0 residues processed: 466 average time/residue: 0.2404 time to fit residues: 144.1396 Evaluate side-chains 390 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 390 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 56 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN D 458 GLN ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 507 GLN E 512 ASN F 438 GLN ** F 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 512 ASN J 512 ASN ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN ** L 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 512 ASN L 514 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 2.0373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8328 Z= 0.358 Angle : 0.868 8.070 11184 Z= 0.465 Chirality : 0.047 0.187 1332 Planarity : 0.006 0.066 1440 Dihedral : 5.598 25.387 1092 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 23.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.50 (0.24), residues: 1020 helix: -0.63 (0.16), residues: 888 sheet: None (None), residues: 0 loop : -2.38 (0.49), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 439 PHE 0.020 0.003 PHE G 501 TYR 0.026 0.003 TYR L 474 ARG 0.011 0.001 ARG H 466 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 476 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 GLN cc_start: 0.9066 (mp10) cc_final: 0.8812 (mp10) REVERT: A 446 ASP cc_start: 0.8818 (t0) cc_final: 0.8464 (t0) REVERT: A 461 ASP cc_start: 0.8985 (m-30) cc_final: 0.8726 (t70) REVERT: A 472 GLU cc_start: 0.9010 (mp0) cc_final: 0.8798 (mp0) REVERT: A 492 ASP cc_start: 0.9206 (m-30) cc_final: 0.8979 (m-30) REVERT: A 500 GLU cc_start: 0.8602 (pm20) cc_final: 0.8154 (pm20) REVERT: A 513 LYS cc_start: 0.9188 (mmpt) cc_final: 0.8961 (mmmt) REVERT: B 445 GLU cc_start: 0.8358 (tp30) cc_final: 0.7636 (tp30) REVERT: B 472 GLU cc_start: 0.8493 (pm20) cc_final: 0.7910 (pt0) REVERT: B 475 GLU cc_start: 0.8795 (pt0) cc_final: 0.8560 (pt0) REVERT: B 479 THR cc_start: 0.8995 (t) cc_final: 0.8640 (p) REVERT: B 480 LYS cc_start: 0.9201 (mmmm) cc_final: 0.8919 (mmmm) REVERT: B 492 ASP cc_start: 0.9171 (m-30) cc_final: 0.8727 (m-30) REVERT: C 461 ASP cc_start: 0.8959 (m-30) cc_final: 0.8707 (m-30) REVERT: C 470 MET cc_start: 0.8742 (mtm) cc_final: 0.8142 (mtt) REVERT: C 472 GLU cc_start: 0.8415 (tt0) cc_final: 0.7795 (tt0) REVERT: C 473 ASP cc_start: 0.9488 (m-30) cc_final: 0.9166 (m-30) REVERT: C 475 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8678 (tm-30) REVERT: C 476 LEU cc_start: 0.9261 (mt) cc_final: 0.8830 (mt) REVERT: C 489 GLN cc_start: 0.8594 (mp10) cc_final: 0.7991 (mp10) REVERT: D 441 GLN cc_start: 0.8720 (tp-100) cc_final: 0.8428 (tm-30) REVERT: D 461 ASP cc_start: 0.9332 (m-30) cc_final: 0.8988 (m-30) REVERT: D 470 MET cc_start: 0.8819 (ptt) cc_final: 0.7987 (ppp) REVERT: D 474 TYR cc_start: 0.9202 (t80) cc_final: 0.8911 (t80) REVERT: D 480 LYS cc_start: 0.9258 (mmtp) cc_final: 0.8987 (mmmm) REVERT: E 441 GLN cc_start: 0.9075 (mt0) cc_final: 0.8780 (mp10) REVERT: E 443 LYS cc_start: 0.9457 (ptpt) cc_final: 0.9151 (ptpp) REVERT: E 446 ASP cc_start: 0.9351 (m-30) cc_final: 0.9141 (m-30) REVERT: E 461 ASP cc_start: 0.8783 (m-30) cc_final: 0.7714 (t70) REVERT: E 465 SER cc_start: 0.9416 (m) cc_final: 0.9160 (p) REVERT: E 466 ARG cc_start: 0.8982 (ptp90) cc_final: 0.8540 (mtm-85) REVERT: E 470 MET cc_start: 0.8129 (ptp) cc_final: 0.7638 (ptp) REVERT: E 480 LYS cc_start: 0.8966 (mtpt) cc_final: 0.8734 (ttmm) REVERT: E 492 ASP cc_start: 0.9327 (m-30) cc_final: 0.9106 (m-30) REVERT: E 494 THR cc_start: 0.9646 (m) cc_final: 0.9440 (m) REVERT: E 495 ASP cc_start: 0.9167 (m-30) cc_final: 0.8841 (m-30) REVERT: E 501 PHE cc_start: 0.8909 (t80) cc_final: 0.8322 (t80) REVERT: F 438 GLN cc_start: 0.9088 (mp10) cc_final: 0.8707 (mp10) REVERT: F 450 GLN cc_start: 0.8762 (mt0) cc_final: 0.8460 (mm-40) REVERT: G 441 GLN cc_start: 0.8432 (tm-30) cc_final: 0.8204 (tm-30) REVERT: G 446 ASP cc_start: 0.8987 (m-30) cc_final: 0.8216 (m-30) REVERT: G 461 ASP cc_start: 0.9200 (m-30) cc_final: 0.8927 (m-30) REVERT: G 468 LEU cc_start: 0.9156 (mt) cc_final: 0.8935 (mp) REVERT: G 471 LYS cc_start: 0.8135 (mmpt) cc_final: 0.7877 (mmmm) REVERT: G 475 GLU cc_start: 0.8001 (mp0) cc_final: 0.7662 (pt0) REVERT: G 480 LYS cc_start: 0.8839 (ttmm) cc_final: 0.8468 (ttmm) REVERT: G 485 SER cc_start: 0.8877 (m) cc_final: 0.8429 (p) REVERT: G 489 GLN cc_start: 0.7803 (pm20) cc_final: 0.7471 (pm20) REVERT: G 509 LEU cc_start: 0.9182 (tp) cc_final: 0.8897 (tt) REVERT: H 446 ASP cc_start: 0.9131 (m-30) cc_final: 0.8893 (m-30) REVERT: H 470 MET cc_start: 0.8722 (mpp) cc_final: 0.7086 (mtm) REVERT: H 473 ASP cc_start: 0.8947 (m-30) cc_final: 0.8196 (m-30) REVERT: H 476 LEU cc_start: 0.9343 (mt) cc_final: 0.9117 (mt) REVERT: H 485 SER cc_start: 0.9269 (m) cc_final: 0.8856 (p) REVERT: H 486 LYS cc_start: 0.9181 (mtpp) cc_final: 0.8685 (mmtm) REVERT: H 489 GLN cc_start: 0.7315 (pm20) cc_final: 0.7084 (pm20) REVERT: H 500 GLU cc_start: 0.8665 (mp0) cc_final: 0.8292 (pm20) REVERT: H 515 MET cc_start: 0.4838 (mmp) cc_final: 0.4353 (mmp) REVERT: I 450 GLN cc_start: 0.8770 (tt0) cc_final: 0.8381 (tt0) REVERT: I 453 GLU cc_start: 0.9147 (tm-30) cc_final: 0.8826 (tm-30) REVERT: I 478 SER cc_start: 0.9626 (t) cc_final: 0.9365 (p) REVERT: I 480 LYS cc_start: 0.9028 (mmtm) cc_final: 0.8758 (mttt) REVERT: I 484 THR cc_start: 0.9478 (m) cc_final: 0.9146 (p) REVERT: I 486 LYS cc_start: 0.9287 (mtpp) cc_final: 0.8903 (mttm) REVERT: I 515 MET cc_start: 0.5998 (tpt) cc_final: 0.5506 (tpp) REVERT: J 441 GLN cc_start: 0.7975 (tm-30) cc_final: 0.7543 (tm-30) REVERT: J 451 MET cc_start: 0.9190 (tpp) cc_final: 0.8796 (tpp) REVERT: J 453 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8624 (tm-30) REVERT: J 467 ASP cc_start: 0.8848 (p0) cc_final: 0.8162 (p0) REVERT: J 470 MET cc_start: 0.8698 (mtt) cc_final: 0.8343 (mtt) REVERT: J 471 LYS cc_start: 0.9201 (mtmt) cc_final: 0.8916 (mtmt) REVERT: J 494 THR cc_start: 0.9685 (m) cc_final: 0.9294 (m) REVERT: J 495 ASP cc_start: 0.9412 (m-30) cc_final: 0.9190 (m-30) REVERT: J 501 PHE cc_start: 0.9158 (t80) cc_final: 0.8439 (t80) REVERT: K 444 ARG cc_start: 0.7356 (ttm170) cc_final: 0.6794 (ptt-90) REVERT: K 452 THR cc_start: 0.9190 (p) cc_final: 0.8902 (p) REVERT: K 468 LEU cc_start: 0.9277 (mm) cc_final: 0.8918 (mp) REVERT: K 469 ILE cc_start: 0.9402 (tt) cc_final: 0.8908 (tt) REVERT: K 470 MET cc_start: 0.7350 (mtm) cc_final: 0.7102 (mtt) REVERT: K 471 LYS cc_start: 0.9373 (mmtm) cc_final: 0.9099 (tttm) REVERT: K 479 THR cc_start: 0.9214 (t) cc_final: 0.9004 (p) REVERT: K 501 PHE cc_start: 0.8920 (t80) cc_final: 0.8694 (t80) REVERT: K 507 GLN cc_start: 0.9312 (tm-30) cc_final: 0.8770 (tm-30) REVERT: L 445 GLU cc_start: 0.8977 (pm20) cc_final: 0.8573 (pm20) REVERT: L 446 ASP cc_start: 0.9118 (m-30) cc_final: 0.8780 (m-30) REVERT: L 451 MET cc_start: 0.8967 (tpp) cc_final: 0.8746 (tpp) REVERT: L 460 LEU cc_start: 0.9479 (mp) cc_final: 0.9275 (mp) REVERT: L 469 ILE cc_start: 0.9130 (tt) cc_final: 0.8749 (tt) REVERT: L 480 LYS cc_start: 0.9425 (mmtm) cc_final: 0.8769 (mmmm) REVERT: L 486 LYS cc_start: 0.9330 (mttp) cc_final: 0.8998 (mtmm) REVERT: L 489 GLN cc_start: 0.9399 (mm-40) cc_final: 0.9105 (mp10) REVERT: L 492 ASP cc_start: 0.9263 (m-30) cc_final: 0.9019 (m-30) REVERT: L 501 PHE cc_start: 0.8704 (t80) cc_final: 0.8260 (t80) outliers start: 0 outliers final: 0 residues processed: 476 average time/residue: 0.2159 time to fit residues: 134.8840 Evaluate side-chains 401 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 401 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 63 optimal weight: 0.0870 chunk 95 optimal weight: 0.0970 chunk 88 optimal weight: 20.0000 chunk 76 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- 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 ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 489 GLN E 512 ASN F 441 GLN ** F 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 512 ASN J 512 ASN K 512 ASN ** L 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 512 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 2.0603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8328 Z= 0.259 Angle : 0.851 9.622 11184 Z= 0.442 Chirality : 0.046 0.169 1332 Planarity : 0.006 0.099 1440 Dihedral : 5.414 24.415 1092 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 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: -0.74 (0.25), residues: 1020 helix: -0.20 (0.17), residues: 852 sheet: None (None), residues: 0 loop : -1.27 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 439 PHE 0.012 0.002 PHE H 501 TYR 0.017 0.002 TYR H 474 ARG 0.013 0.001 ARG B 444 ********************** 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 480 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 ASP cc_start: 0.8533 (t0) cc_final: 0.8126 (t0) REVERT: A 458 GLN cc_start: 0.9231 (pt0) cc_final: 0.9008 (pt0) REVERT: A 461 ASP cc_start: 0.8987 (m-30) cc_final: 0.8675 (t70) REVERT: A 470 MET cc_start: 0.9270 (mtt) cc_final: 0.8929 (mtt) REVERT: A 492 ASP cc_start: 0.9135 (m-30) cc_final: 0.8896 (m-30) REVERT: A 500 GLU cc_start: 0.8539 (pm20) cc_final: 0.8239 (pm20) REVERT: A 507 GLN cc_start: 0.8968 (pp30) cc_final: 0.8760 (pp30) REVERT: A 513 LYS cc_start: 0.9163 (mmpt) cc_final: 0.8939 (mmmt) REVERT: B 441 GLN cc_start: 0.8442 (mp10) cc_final: 0.7990 (mp10) REVERT: B 445 GLU cc_start: 0.8399 (tp30) cc_final: 0.7919 (tp30) REVERT: B 472 GLU cc_start: 0.8477 (pm20) cc_final: 0.7973 (pm20) REVERT: B 473 ASP cc_start: 0.9515 (m-30) cc_final: 0.9197 (m-30) REVERT: B 500 GLU cc_start: 0.7971 (pm20) cc_final: 0.7757 (pm20) REVERT: C 447 ILE cc_start: 0.8804 (mt) cc_final: 0.8475 (mt) REVERT: C 461 ASP cc_start: 0.9152 (m-30) cc_final: 0.8838 (m-30) REVERT: C 470 MET cc_start: 0.8816 (mtm) cc_final: 0.8264 (mtm) REVERT: C 471 LYS cc_start: 0.9031 (tmtt) cc_final: 0.8520 (tmtt) REVERT: D 461 ASP cc_start: 0.9256 (m-30) cc_final: 0.8368 (t70) REVERT: D 466 ARG cc_start: 0.8828 (mpp80) cc_final: 0.8542 (mpp80) REVERT: D 470 MET cc_start: 0.8187 (ptt) cc_final: 0.7908 (ppp) REVERT: D 480 LYS cc_start: 0.9267 (mmtp) cc_final: 0.8854 (mmmm) REVERT: D 495 ASP cc_start: 0.9132 (m-30) cc_final: 0.8929 (m-30) REVERT: E 441 GLN cc_start: 0.8884 (mt0) cc_final: 0.8593 (mp10) REVERT: E 443 LYS cc_start: 0.9440 (ptpt) cc_final: 0.9118 (ptpp) REVERT: E 446 ASP cc_start: 0.9280 (m-30) cc_final: 0.9078 (m-30) REVERT: E 461 ASP cc_start: 0.8705 (m-30) cc_final: 0.7869 (t70) REVERT: E 465 SER cc_start: 0.9320 (m) cc_final: 0.9103 (p) REVERT: E 466 ARG cc_start: 0.8947 (ptp90) cc_final: 0.8414 (mtm-85) REVERT: E 470 MET cc_start: 0.8571 (ptp) cc_final: 0.8298 (ptp) REVERT: E 471 LYS cc_start: 0.9323 (pttt) cc_final: 0.8793 (tmtt) REVERT: E 476 LEU cc_start: 0.9138 (mt) cc_final: 0.8686 (mt) REVERT: E 480 LYS cc_start: 0.9182 (mtpt) cc_final: 0.8675 (mtpp) REVERT: E 489 GLN cc_start: 0.9081 (mm110) cc_final: 0.8704 (mp10) REVERT: E 494 THR cc_start: 0.9561 (m) cc_final: 0.9131 (m) REVERT: E 501 PHE cc_start: 0.8922 (t80) cc_final: 0.7849 (t80) REVERT: E 507 GLN cc_start: 0.9431 (tp40) cc_final: 0.9191 (tp-100) REVERT: F 438 GLN cc_start: 0.9017 (mp10) cc_final: 0.8815 (mp10) REVERT: F 447 ILE cc_start: 0.9383 (tp) cc_final: 0.9144 (mm) REVERT: F 450 GLN cc_start: 0.8661 (mt0) cc_final: 0.8372 (mm-40) REVERT: F 461 ASP cc_start: 0.9238 (t70) cc_final: 0.8980 (m-30) REVERT: F 467 ASP cc_start: 0.9171 (t0) cc_final: 0.8603 (m-30) REVERT: F 480 LYS cc_start: 0.8257 (mtmt) cc_final: 0.8049 (ptpt) REVERT: F 513 LYS cc_start: 0.8595 (mmtt) cc_final: 0.8357 (mmmt) REVERT: G 446 ASP cc_start: 0.8954 (m-30) cc_final: 0.8181 (m-30) REVERT: G 461 ASP cc_start: 0.9050 (m-30) cc_final: 0.7827 (t70) REVERT: G 468 LEU cc_start: 0.9163 (mt) cc_final: 0.8850 (mp) REVERT: G 474 TYR cc_start: 0.6946 (t80) cc_final: 0.6719 (t80) REVERT: G 475 GLU cc_start: 0.7892 (mp0) cc_final: 0.7433 (tm-30) REVERT: H 432 SER cc_start: 0.8773 (t) cc_final: 0.8442 (p) REVERT: H 445 GLU cc_start: 0.8876 (pm20) cc_final: 0.8662 (pm20) REVERT: H 470 MET cc_start: 0.8762 (mpp) cc_final: 0.6922 (mtm) REVERT: H 473 ASP cc_start: 0.8879 (m-30) cc_final: 0.8008 (m-30) REVERT: H 476 LEU cc_start: 0.9392 (mt) cc_final: 0.9155 (mt) REVERT: H 485 SER cc_start: 0.9272 (m) cc_final: 0.8894 (p) REVERT: H 486 LYS cc_start: 0.9230 (mtpp) cc_final: 0.8844 (mttm) REVERT: H 500 GLU cc_start: 0.8606 (mp0) cc_final: 0.8222 (pm20) REVERT: H 515 MET cc_start: 0.4824 (mmp) cc_final: 0.4608 (mmp) REVERT: I 450 GLN cc_start: 0.8410 (tt0) cc_final: 0.8092 (tt0) REVERT: I 478 SER cc_start: 0.9550 (t) cc_final: 0.9331 (p) REVERT: I 486 LYS cc_start: 0.9296 (mtpp) cc_final: 0.8997 (mttm) REVERT: I 515 MET cc_start: 0.6117 (tpt) cc_final: 0.5605 (tpp) REVERT: J 441 GLN cc_start: 0.7979 (tm-30) cc_final: 0.7600 (tm-30) REVERT: J 451 MET cc_start: 0.9034 (tpp) cc_final: 0.8690 (tpp) REVERT: J 453 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8622 (tm-30) REVERT: J 464 LEU cc_start: 0.9220 (tp) cc_final: 0.8901 (tt) REVERT: J 467 ASP cc_start: 0.8787 (p0) cc_final: 0.8517 (p0) REVERT: J 475 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8649 (pt0) REVERT: J 480 LYS cc_start: 0.9207 (mmtt) cc_final: 0.8795 (mttm) REVERT: J 494 THR cc_start: 0.9609 (m) cc_final: 0.9340 (p) REVERT: J 495 ASP cc_start: 0.9380 (m-30) cc_final: 0.8972 (m-30) REVERT: J 501 PHE cc_start: 0.9063 (t80) cc_final: 0.8514 (t80) REVERT: K 444 ARG cc_start: 0.7230 (ttm170) cc_final: 0.6552 (ptt180) REVERT: K 452 THR cc_start: 0.9145 (p) cc_final: 0.8892 (p) REVERT: K 471 LYS cc_start: 0.9399 (mmtm) cc_final: 0.9095 (pttt) REVERT: L 441 GLN cc_start: 0.8969 (tt0) cc_final: 0.8260 (tp-100) REVERT: L 445 GLU cc_start: 0.8941 (pm20) cc_final: 0.8669 (pm20) REVERT: L 451 MET cc_start: 0.9162 (tpp) cc_final: 0.8912 (tpp) REVERT: L 469 ILE cc_start: 0.8927 (tt) cc_final: 0.8073 (tt) REVERT: L 480 LYS cc_start: 0.9442 (mmtm) cc_final: 0.8945 (mmmm) REVERT: L 486 LYS cc_start: 0.9351 (mttp) cc_final: 0.9036 (mtmm) REVERT: L 489 GLN cc_start: 0.9329 (mm-40) cc_final: 0.8812 (mp10) REVERT: L 492 ASP cc_start: 0.9210 (m-30) cc_final: 0.8971 (m-30) REVERT: L 500 GLU cc_start: 0.9078 (tp30) cc_final: 0.8871 (mm-30) REVERT: L 501 PHE cc_start: 0.8911 (t80) cc_final: 0.8380 (t80) outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 0.2264 time to fit residues: 143.7478 Evaluate side-chains 413 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 413 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 449 ASN ** D 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 438 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** ** H 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 512 ASN I 489 GLN J 512 ASN K 512 ASN ** L 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 512 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.064767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.051488 restraints weight = 37292.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.053345 restraints weight = 24877.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.054764 restraints weight = 18488.517| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 2.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8328 Z= 0.253 Angle : 0.840 8.073 11184 Z= 0.442 Chirality : 0.046 0.191 1332 Planarity : 0.007 0.146 1440 Dihedral : 5.412 31.579 1092 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 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: -0.71 (0.25), residues: 1020 helix: -0.20 (0.16), residues: 852 sheet: None (None), residues: 0 loop : -1.11 (0.53), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 439 PHE 0.026 0.003 PHE G 501 TYR 0.007 0.001 TYR K 474 ARG 0.014 0.001 ARG B 444 =============================================================================== Job complete usr+sys time: 2511.76 seconds wall clock time: 45 minutes 16.89 seconds (2716.89 seconds total)