Starting phenix.real_space_refine on Mon Mar 11 12:53:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yrn_6842/03_2024/5yrn_6842.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yrn_6842/03_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_6842/03_2024/5yrn_6842.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yrn_6842/03_2024/5yrn_6842.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yrn_6842/03_2024/5yrn_6842.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yrn_6842/03_2024/5yrn_6842.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8280 Number of models: 1 Model: "" Number of chains: 12 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} Chain: "B" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "D" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "E" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "F" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "H" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "I" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "J" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "K" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "L" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Time building chain proxies: 4.78, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 3.17 Conformation dependent library (CDL) restraints added in 1.5 seconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 87.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 430 through 443 removed outlier: 3.773A pdb=" N GLN A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 451 Processing helix chain 'A' and resid 452 through 466 removed outlier: 3.573A pdb=" N SER A 459 " --> pdb=" O CYS A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 479 Processing helix chain 'A' and resid 482 through 497 removed outlier: 3.523A pdb=" N GLN A 489 " --> pdb=" O SER A 485 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 490 " --> pdb=" O LYS A 486 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A 496 " --> pdb=" O ASP A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 512 removed outlier: 3.773A pdb=" N VAL A 504 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE A 505 " --> pdb=" O PHE A 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 removed outlier: 3.772A pdb=" N GLN B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 451 Processing helix chain 'B' and resid 452 through 466 removed outlier: 3.574A pdb=" N SER B 459 " --> pdb=" O CYS B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 479 Processing helix chain 'B' and resid 482 through 497 removed outlier: 3.522A pdb=" N GLN B 489 " --> pdb=" O SER B 485 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 490 " --> pdb=" O LYS B 486 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 496 " --> pdb=" O ASP B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 512 removed outlier: 3.774A pdb=" N VAL B 504 " --> pdb=" O GLU B 500 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE B 505 " --> pdb=" O PHE B 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 443 removed outlier: 3.773A pdb=" N GLN C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 451 Processing helix chain 'C' and resid 452 through 466 removed outlier: 3.573A pdb=" N SER C 459 " --> pdb=" O CYS C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 479 Processing helix chain 'C' and resid 482 through 497 removed outlier: 3.523A pdb=" N GLN C 489 " --> pdb=" O SER C 485 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 490 " --> pdb=" O LYS C 486 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE C 496 " --> pdb=" O ASP C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 512 removed outlier: 3.773A pdb=" N VAL C 504 " --> pdb=" O GLU C 500 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE C 505 " --> pdb=" O PHE C 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 443 removed outlier: 3.772A pdb=" N GLN D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 451 Processing helix chain 'D' and resid 452 through 466 removed outlier: 3.573A pdb=" N SER D 459 " --> pdb=" O CYS D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 479 Processing helix chain 'D' and resid 482 through 497 removed outlier: 3.522A pdb=" N GLN D 489 " --> pdb=" O SER D 485 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU D 490 " --> pdb=" O LYS D 486 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE D 496 " --> pdb=" O ASP D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 512 removed outlier: 3.773A pdb=" N VAL D 504 " --> pdb=" O GLU D 500 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE D 505 " --> pdb=" O PHE D 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 443 removed outlier: 3.773A pdb=" N GLN E 437 " --> pdb=" O ALA E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 451 Processing helix chain 'E' and resid 452 through 466 removed outlier: 3.573A pdb=" N SER E 459 " --> pdb=" O CYS E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 479 Processing helix chain 'E' and resid 482 through 497 removed outlier: 3.523A pdb=" N GLN E 489 " --> pdb=" O SER E 485 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU E 490 " --> pdb=" O LYS E 486 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP E 495 " --> pdb=" O LEU E 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE E 496 " --> pdb=" O ASP E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 512 removed outlier: 3.773A pdb=" N VAL E 504 " --> pdb=" O GLU E 500 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE E 505 " --> pdb=" O PHE E 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 443 removed outlier: 3.773A pdb=" N GLN F 437 " --> pdb=" O ALA F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 444 through 451 Processing helix chain 'F' and resid 452 through 466 removed outlier: 3.573A pdb=" N SER F 459 " --> pdb=" O CYS F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 479 Processing helix chain 'F' and resid 482 through 497 removed outlier: 3.523A pdb=" N GLN F 489 " --> pdb=" O SER F 485 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU F 490 " --> pdb=" O LYS F 486 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP F 495 " --> pdb=" O LEU F 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE F 496 " --> pdb=" O ASP F 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 512 removed outlier: 3.774A pdb=" N VAL F 504 " --> pdb=" O GLU F 500 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE F 505 " --> pdb=" O PHE F 501 " (cutoff:3.500A) Processing helix chain 'G' and resid 431 through 443 removed outlier: 3.772A pdb=" N GLN G 437 " --> pdb=" O ALA G 433 " (cutoff:3.500A) Processing helix chain 'G' and resid 444 through 451 Processing helix chain 'G' and resid 452 through 466 removed outlier: 3.574A pdb=" N SER G 459 " --> pdb=" O CYS G 455 " (cutoff:3.500A) Processing helix chain 'G' and resid 470 through 479 Processing helix chain 'G' and resid 482 through 497 removed outlier: 3.523A pdb=" N GLN G 489 " --> pdb=" O SER G 485 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU G 490 " --> pdb=" O LYS G 486 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP G 495 " --> pdb=" O LEU G 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE G 496 " --> pdb=" O ASP G 492 " (cutoff:3.500A) Processing helix chain 'G' and resid 499 through 512 removed outlier: 3.774A pdb=" N VAL G 504 " --> pdb=" O GLU G 500 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE G 505 " --> pdb=" O PHE G 501 " (cutoff:3.500A) Processing helix chain 'H' and resid 431 through 443 removed outlier: 3.773A pdb=" N GLN H 437 " --> pdb=" O ALA H 433 " (cutoff:3.500A) Processing helix chain 'H' and resid 444 through 451 Processing helix chain 'H' and resid 452 through 466 removed outlier: 3.573A pdb=" N SER H 459 " --> pdb=" O CYS H 455 " (cutoff:3.500A) Processing helix chain 'H' and resid 470 through 479 Processing helix chain 'H' and resid 482 through 497 removed outlier: 3.522A pdb=" N GLN H 489 " --> pdb=" O SER H 485 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU H 490 " --> pdb=" O LYS H 486 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP H 495 " --> pdb=" O LEU H 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE H 496 " --> pdb=" O ASP H 492 " (cutoff:3.500A) Processing helix chain 'H' and resid 499 through 512 removed outlier: 3.773A pdb=" N VAL H 504 " --> pdb=" O GLU H 500 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE H 505 " --> pdb=" O PHE H 501 " (cutoff:3.500A) Processing helix chain 'I' and resid 431 through 443 removed outlier: 3.773A pdb=" N GLN I 437 " --> pdb=" O ALA I 433 " (cutoff:3.500A) Processing helix chain 'I' and resid 444 through 451 Processing helix chain 'I' and resid 452 through 466 removed outlier: 3.573A pdb=" N SER I 459 " --> pdb=" O CYS I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 470 through 479 Processing helix chain 'I' and resid 482 through 497 removed outlier: 3.523A pdb=" N GLN I 489 " --> pdb=" O SER I 485 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU I 490 " --> pdb=" O LYS I 486 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP I 495 " --> pdb=" O LEU I 491 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE I 496 " --> pdb=" O ASP I 492 " (cutoff:3.500A) Processing helix chain 'I' and resid 499 through 512 removed outlier: 3.774A pdb=" N VAL I 504 " --> pdb=" O GLU I 500 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE I 505 " --> pdb=" O PHE I 501 " (cutoff:3.500A) Processing helix chain 'J' and resid 431 through 443 removed outlier: 3.772A pdb=" N GLN J 437 " --> pdb=" O ALA J 433 " (cutoff:3.500A) Processing helix chain 'J' and resid 444 through 451 Processing helix chain 'J' and resid 452 through 466 removed outlier: 3.574A pdb=" N SER J 459 " --> pdb=" O CYS J 455 " (cutoff:3.500A) Processing helix chain 'J' and resid 470 through 479 Processing helix chain 'J' and resid 482 through 497 removed outlier: 3.523A pdb=" N GLN J 489 " --> pdb=" O SER J 485 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU J 490 " --> pdb=" O LYS J 486 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP J 495 " --> pdb=" O LEU J 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE J 496 " --> pdb=" O ASP J 492 " (cutoff:3.500A) Processing helix chain 'J' and resid 499 through 512 removed outlier: 3.773A pdb=" N VAL J 504 " --> pdb=" O GLU J 500 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE J 505 " --> pdb=" O PHE J 501 " (cutoff:3.500A) Processing helix chain 'K' and resid 431 through 443 removed outlier: 3.772A pdb=" N GLN K 437 " --> pdb=" O ALA K 433 " (cutoff:3.500A) Processing helix chain 'K' and resid 444 through 451 Processing helix chain 'K' and resid 452 through 466 removed outlier: 3.573A pdb=" N SER K 459 " --> pdb=" O CYS K 455 " (cutoff:3.500A) Processing helix chain 'K' and resid 470 through 479 Processing helix chain 'K' and resid 482 through 497 removed outlier: 3.522A pdb=" N GLN K 489 " --> pdb=" O SER K 485 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU K 490 " --> pdb=" O LYS K 486 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP K 495 " --> pdb=" O LEU K 491 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE K 496 " --> pdb=" O ASP K 492 " (cutoff:3.500A) Processing helix chain 'K' and resid 499 through 512 removed outlier: 3.773A pdb=" N VAL K 504 " --> pdb=" O GLU K 500 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE K 505 " --> pdb=" O PHE K 501 " (cutoff:3.500A) Processing helix chain 'L' and resid 431 through 443 removed outlier: 3.773A pdb=" N GLN L 437 " --> pdb=" O ALA L 433 " (cutoff:3.500A) Processing helix chain 'L' and resid 444 through 451 Processing helix chain 'L' and resid 452 through 466 removed outlier: 3.573A pdb=" N SER L 459 " --> pdb=" O CYS L 455 " (cutoff:3.500A) Processing helix chain 'L' and resid 470 through 479 Processing helix chain 'L' and resid 482 through 497 removed outlier: 3.522A pdb=" N GLN L 489 " --> pdb=" O SER L 485 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU L 490 " --> pdb=" O LYS L 486 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP L 495 " --> pdb=" O LEU L 491 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE L 496 " --> pdb=" O ASP L 492 " (cutoff:3.500A) Processing helix chain 'L' and resid 499 through 512 removed outlier: 3.773A pdb=" N VAL L 504 " --> pdb=" O GLU L 500 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE L 505 " --> pdb=" O PHE L 501 " (cutoff:3.500A) 529 hydrogen bonds defined for protein. 1587 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 3.43 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: 100.33 - 107.04: 148 107.04 - 113.74: 5019 113.74 - 120.45: 3096 120.45 - 127.16: 2885 127.16 - 133.87: 36 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 2.520 nonbonded pdb=" NE2 GLN C 441 " pdb=" OD1 ASP C 495 " model vdw 2.393 2.520 nonbonded pdb=" NE2 GLN E 441 " pdb=" OD1 ASP E 495 " model vdw 2.393 2.520 nonbonded pdb=" NE2 GLN F 441 " pdb=" OD1 ASP F 495 " model vdw 2.393 2.520 nonbonded pdb=" NE2 GLN I 441 " pdb=" OD1 ASP I 495 " model vdw 2.393 2.520 ... (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 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.190 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 25.040 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.360 ------------------------------------------------------------------------------- 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 : 1.107 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: 0.3073 time to fit residues: 156.8587 Evaluate side-chains 217 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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: 0.6980 chunk 72 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 87 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 GLN A 512 ASN B 497 GLN ** C 437 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 497 GLN D 512 ASN E 497 GLN ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 514 GLN ** H 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 514 GLN I 458 GLN K 514 GLN ** L 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6335 moved from start: 0.7488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8328 Z= 0.239 Angle : 0.738 8.642 11184 Z= 0.392 Chirality : 0.043 0.209 1332 Planarity : 0.005 0.054 1440 Dihedral : 5.558 21.663 1092 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % 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: -2.21 (0.22), residues: 1020 helix: -1.28 (0.14), residues: 912 sheet: None (None), residues: 0 loop : -1.03 (0.53), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 439 PHE 0.008 0.002 PHE D 501 TYR 0.007 0.001 TYR E 474 ARG 0.014 0.001 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 339 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 1.300 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 448 VAL cc_start: 0.8559 (t) cc_final: 0.8342 (p) REVERT: A 492 ASP cc_start: 0.8172 (m-30) cc_final: 0.7845 (m-30) REVERT: A 494 THR cc_start: 0.9206 (m) cc_final: 0.8920 (m) REVERT: B 460 LEU cc_start: 0.7614 (mt) cc_final: 0.7196 (mt) REVERT: B 463 LEU cc_start: 0.8893 (mt) cc_final: 0.8234 (mt) REVERT: B 470 MET cc_start: 0.7807 (mtm) cc_final: 0.7540 (mtt) REVERT: B 503 LYS cc_start: 0.9144 (ttmt) cc_final: 0.8802 (tptt) REVERT: C 479 THR cc_start: 0.5701 (m) cc_final: 0.5183 (m) REVERT: C 503 LYS cc_start: 0.8282 (ttmt) cc_final: 0.7802 (tptt) REVERT: C 513 LYS cc_start: 0.8358 (mmmt) cc_final: 0.8054 (tppt) REVERT: D 446 ASP cc_start: 0.8794 (m-30) cc_final: 0.8531 (m-30) REVERT: D 479 THR cc_start: 0.6739 (t) cc_final: 0.6360 (t) REVERT: D 480 LYS cc_start: 0.8744 (mttp) cc_final: 0.8474 (mtpp) REVERT: D 488 ARG cc_start: 0.8591 (mmm-85) cc_final: 0.8259 (mtt90) REVERT: D 503 LYS cc_start: 0.8716 (pttm) cc_final: 0.7605 (tptt) REVERT: D 513 LYS cc_start: 0.8559 (pptt) cc_final: 0.8064 (tptp) REVERT: E 461 ASP cc_start: 0.8986 (m-30) cc_final: 0.8447 (t70) REVERT: E 470 MET cc_start: 0.6994 (ptp) cc_final: 0.6663 (ptp) REVERT: E 483 ARG cc_start: 0.7452 (mtt180) cc_final: 0.6952 (ttm-80) REVERT: F 450 GLN cc_start: 0.7633 (mm-40) cc_final: 0.7414 (mm110) REVERT: H 470 MET cc_start: 0.7295 (mpp) cc_final: 0.7075 (mpp) REVERT: H 471 LYS cc_start: 0.7775 (tttt) cc_final: 0.7404 (pttt) REVERT: H 477 VAL cc_start: 0.6831 (t) cc_final: 0.6542 (t) REVERT: J 435 ILE cc_start: 0.7364 (mt) cc_final: 0.6828 (tp) REVERT: J 445 GLU cc_start: 0.7395 (mp0) cc_final: 0.6540 (mp0) REVERT: J 474 TYR cc_start: 0.7978 (t80) cc_final: 0.7574 (t80) REVERT: J 499 GLU cc_start: 0.8077 (pp20) cc_final: 0.7339 (tp30) REVERT: J 501 PHE cc_start: 0.7353 (t80) cc_final: 0.7126 (t80) REVERT: J 503 LYS cc_start: 0.7777 (pptt) cc_final: 0.7044 (ptpp) REVERT: L 430 THR cc_start: 0.8273 (p) cc_final: 0.8003 (p) REVERT: L 453 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8173 (tm-30) REVERT: L 480 LYS cc_start: 0.7737 (mmtt) cc_final: 0.6977 (mmmm) REVERT: L 489 GLN cc_start: 0.8940 (mm110) cc_final: 0.8368 (mt0) REVERT: L 501 PHE cc_start: 0.8715 (t80) cc_final: 0.8489 (t80) REVERT: L 509 LEU cc_start: 0.9005 (tt) cc_final: 0.8691 (pp) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.2730 time to fit residues: 117.3029 Evaluate side-chains 241 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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: 5.9990 chunk 72 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 24 optimal weight: 30.0000 chunk 87 optimal weight: 0.9990 chunk 94 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN C 437 GLN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 GLN ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 ASN G 512 ASN H 507 GLN ** H 512 ASN ** 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 497 GLN ** J 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 437 GLN ** K 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN L 497 GLN ** L 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 1.5445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 8328 Z= 0.424 Angle : 0.992 9.729 11184 Z= 0.536 Chirality : 0.050 0.201 1332 Planarity : 0.008 0.084 1440 Dihedral : 6.624 26.588 1092 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 28.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.42 % Allowed : 8.76 % Favored : 90.82 % 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: -2.63 (0.22), residues: 1020 helix: -1.45 (0.15), residues: 936 sheet: None (None), residues: 0 loop : -2.41 (0.52), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP H 439 PHE 0.029 0.004 PHE H 501 TYR 0.018 0.003 TYR L 474 ARG 0.013 0.002 ARG C 444 *********************** 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 514 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 510 time to evaluate : 0.961 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: 0.9166 (m-30) cc_final: 0.8903 (t0) REVERT: A 461 ASP cc_start: 0.8938 (m-30) cc_final: 0.8360 (t70) REVERT: A 470 MET cc_start: 0.8467 (mtt) cc_final: 0.7704 (mtt) REVERT: A 471 LYS cc_start: 0.9187 (ptpp) cc_final: 0.8684 (ptmm) REVERT: A 472 GLU cc_start: 0.9390 (mp0) cc_final: 0.9109 (mp0) REVERT: A 473 ASP cc_start: 0.9411 (m-30) cc_final: 0.9166 (m-30) REVERT: A 474 TYR cc_start: 0.9323 (t80) cc_final: 0.8994 (t80) REVERT: A 489 GLN cc_start: 0.8960 (tm-30) cc_final: 0.8647 (tm-30) REVERT: A 491 LEU cc_start: 0.9602 (mm) cc_final: 0.9397 (mt) REVERT: B 458 GLN cc_start: 0.9188 (mp-120) cc_final: 0.8890 (pt0) REVERT: B 470 MET cc_start: 0.8530 (mtm) cc_final: 0.8048 (mtt) REVERT: B 480 LYS cc_start: 0.8666 (mttp) cc_final: 0.8208 (mttt) REVERT: B 500 GLU cc_start: 0.8405 (tt0) cc_final: 0.8040 (pm20) REVERT: C 440 ILE cc_start: 0.8973 (mt) cc_final: 0.8110 (mt) REVERT: C 444 ARG cc_start: 0.8411 (mmp-170) cc_final: 0.8084 (ttt-90) REVERT: C 456 LEU cc_start: 0.9563 (tp) cc_final: 0.9052 (tt) REVERT: C 470 MET cc_start: 0.8938 (mtp) cc_final: 0.8625 (mtm) REVERT: C 476 LEU cc_start: 0.9370 (mt) cc_final: 0.9077 (mt) REVERT: C 478 SER cc_start: 0.9438 (t) cc_final: 0.9060 (p) REVERT: C 484 THR cc_start: 0.9112 (p) cc_final: 0.8910 (p) REVERT: C 491 LEU cc_start: 0.8442 (mp) cc_final: 0.7920 (mm) REVERT: C 492 ASP cc_start: 0.8933 (m-30) cc_final: 0.8567 (m-30) REVERT: C 513 LYS cc_start: 0.8667 (mmmt) cc_final: 0.8313 (tppt) REVERT: D 441 GLN cc_start: 0.8683 (tp-100) cc_final: 0.7785 (tm-30) REVERT: D 446 ASP cc_start: 0.9136 (m-30) cc_final: 0.8892 (m-30) REVERT: D 453 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7279 (tm-30) REVERT: D 469 ILE cc_start: 0.8452 (tt) cc_final: 0.7660 (tt) REVERT: D 470 MET cc_start: 0.8542 (ptp) cc_final: 0.8007 (ptp) REVERT: D 471 LYS cc_start: 0.9442 (ttpp) cc_final: 0.9236 (tmtt) REVERT: D 477 VAL cc_start: 0.8889 (t) cc_final: 0.8524 (t) REVERT: D 478 SER cc_start: 0.9209 (t) cc_final: 0.8962 (p) REVERT: D 483 ARG cc_start: 0.8760 (mtt180) cc_final: 0.8070 (ttp80) REVERT: D 496 ILE cc_start: 0.6599 (OUTLIER) cc_final: 0.6045 (mp) REVERT: D 507 GLN cc_start: 0.9153 (tm-30) cc_final: 0.8798 (tp-100) REVERT: E 437 GLN cc_start: 0.9272 (tt0) cc_final: 0.8964 (tt0) REVERT: E 441 GLN cc_start: 0.9006 (mt0) cc_final: 0.8724 (mp10) REVERT: E 473 ASP cc_start: 0.8483 (m-30) cc_final: 0.8257 (m-30) REVERT: E 474 TYR cc_start: 0.9264 (t80) cc_final: 0.9040 (t80) REVERT: E 480 LYS cc_start: 0.8606 (mtpt) cc_final: 0.8216 (ttmm) REVERT: E 483 ARG cc_start: 0.8385 (mtt180) cc_final: 0.8185 (ttm170) REVERT: E 486 LYS cc_start: 0.9071 (mtpt) cc_final: 0.8711 (mtpp) REVERT: E 489 GLN cc_start: 0.8904 (mp10) cc_final: 0.8530 (mp10) REVERT: E 503 LYS cc_start: 0.9513 (pttm) cc_final: 0.9238 (ptpp) REVERT: E 515 MET cc_start: 0.5789 (tpt) cc_final: 0.5554 (tpp) REVERT: F 458 GLN cc_start: 0.9500 (mm110) cc_final: 0.8863 (pt0) REVERT: F 460 LEU cc_start: 0.9023 (mt) cc_final: 0.8805 (mt) REVERT: F 461 ASP cc_start: 0.8713 (t70) cc_final: 0.7984 (t0) REVERT: G 461 ASP cc_start: 0.8804 (m-30) cc_final: 0.8490 (m-30) REVERT: G 467 ASP cc_start: 0.8748 (t70) cc_final: 0.8489 (t0) REVERT: G 468 LEU cc_start: 0.9123 (mt) cc_final: 0.8848 (mt) REVERT: G 475 GLU cc_start: 0.7744 (mp0) cc_final: 0.6892 (pt0) REVERT: G 488 ARG cc_start: 0.8699 (mtt-85) cc_final: 0.8430 (mtt180) REVERT: G 497 GLN cc_start: 0.3881 (mm-40) cc_final: 0.3660 (mm-40) REVERT: G 501 PHE cc_start: 0.6962 (t80) cc_final: 0.6302 (t80) REVERT: G 503 LYS cc_start: 0.9544 (pttm) cc_final: 0.9005 (pttp) REVERT: G 506 VAL cc_start: 0.9350 (t) cc_final: 0.8626 (t) REVERT: G 507 GLN cc_start: 0.9329 (tp-100) cc_final: 0.8979 (mm110) REVERT: H 443 LYS cc_start: 0.9169 (mttt) cc_final: 0.8645 (mtmm) REVERT: H 446 ASP cc_start: 0.8968 (m-30) cc_final: 0.8661 (m-30) REVERT: H 461 ASP cc_start: 0.8509 (t70) cc_final: 0.7999 (t70) REVERT: H 470 MET cc_start: 0.8768 (mpp) cc_final: 0.6940 (mpp) REVERT: H 471 LYS cc_start: 0.8762 (tttt) cc_final: 0.8437 (pttt) REVERT: H 473 ASP cc_start: 0.7845 (m-30) cc_final: 0.6945 (m-30) REVERT: H 485 SER cc_start: 0.8553 (m) cc_final: 0.7693 (p) REVERT: H 489 GLN cc_start: 0.7017 (pm20) cc_final: 0.6711 (pm20) REVERT: H 501 PHE cc_start: 0.8484 (t80) cc_final: 0.8126 (t80) REVERT: H 515 MET cc_start: 0.3820 (mmp) cc_final: 0.3072 (mmt) REVERT: I 476 LEU cc_start: 0.9451 (mt) cc_final: 0.9210 (mt) REVERT: I 480 LYS cc_start: 0.8937 (mmtt) cc_final: 0.8693 (mmmm) REVERT: J 435 ILE cc_start: 0.8119 (mt) cc_final: 0.7917 (mt) REVERT: J 449 ASN cc_start: 0.9144 (m-40) cc_final: 0.8880 (m-40) REVERT: J 469 ILE cc_start: 0.9644 (tt) cc_final: 0.9067 (tt) REVERT: J 470 MET cc_start: 0.9125 (mtm) cc_final: 0.8094 (mtm) REVERT: J 471 LYS cc_start: 0.9198 (mmtm) cc_final: 0.8995 (mtmt) REVERT: J 501 PHE cc_start: 0.8379 (t80) cc_final: 0.8043 (t80) REVERT: K 443 LYS cc_start: 0.5948 (OUTLIER) cc_final: 0.5241 (ptmm) REVERT: K 450 GLN cc_start: 0.8944 (mm-40) cc_final: 0.8594 (mt0) REVERT: K 453 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8921 (tp30) REVERT: K 456 LEU cc_start: 0.9116 (tp) cc_final: 0.8896 (tp) REVERT: K 461 ASP cc_start: 0.8973 (t70) cc_final: 0.8575 (t70) REVERT: K 503 LYS cc_start: 0.9197 (ptmm) cc_final: 0.8941 (ptmm) REVERT: K 507 GLN cc_start: 0.8924 (mt0) cc_final: 0.8683 (tm-30) REVERT: L 441 GLN cc_start: 0.9014 (mt0) cc_final: 0.8271 (tm-30) REVERT: L 475 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7951 (mt-10) REVERT: L 480 LYS cc_start: 0.9541 (mmtt) cc_final: 0.9231 (mmmm) REVERT: L 485 SER cc_start: 0.9628 (m) cc_final: 0.9002 (p) REVERT: L 492 ASP cc_start: 0.9312 (m-30) cc_final: 0.9092 (m-30) outliers start: 4 outliers final: 1 residues processed: 513 average time/residue: 0.2471 time to fit residues: 160.6238 Evaluate side-chains 374 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 371 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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: 6.9990 chunk 45 optimal weight: 0.1980 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 507 GLN ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 ASN ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 ASN ** H 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 512 ASN ** J 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN ** L 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 512 ASN L 514 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 1.6338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 8328 Z= 0.205 Angle : 0.673 8.619 11184 Z= 0.358 Chirality : 0.041 0.158 1332 Planarity : 0.004 0.063 1440 Dihedral : 5.296 19.605 1092 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 3.27 % 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: -0.71 (0.24), residues: 1020 helix: -0.26 (0.16), residues: 852 sheet: None (None), residues: 0 loop : -0.75 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 439 PHE 0.009 0.002 PHE E 501 TYR 0.011 0.001 TYR J 474 ARG 0.007 0.001 ARG I 444 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 481 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 ASP cc_start: 0.9015 (m-30) cc_final: 0.8236 (t70) REVERT: A 468 LEU cc_start: 0.9444 (mm) cc_final: 0.9122 (mm) REVERT: A 470 MET cc_start: 0.8674 (mtt) cc_final: 0.8165 (mtt) REVERT: A 471 LYS cc_start: 0.9071 (ptpp) cc_final: 0.8465 (ttpp) REVERT: A 480 LYS cc_start: 0.9156 (mmmt) cc_final: 0.8722 (mmmt) REVERT: A 486 LYS cc_start: 0.9236 (mtmm) cc_final: 0.8733 (mttp) REVERT: A 489 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8368 (tp40) REVERT: A 491 LEU cc_start: 0.9580 (mm) cc_final: 0.9308 (mp) REVERT: A 492 ASP cc_start: 0.9199 (m-30) cc_final: 0.8969 (m-30) REVERT: B 458 GLN cc_start: 0.9100 (mp-120) cc_final: 0.8823 (pt0) REVERT: B 470 MET cc_start: 0.8466 (mtm) cc_final: 0.8020 (mtt) REVERT: B 476 LEU cc_start: 0.9474 (mt) cc_final: 0.9241 (mt) REVERT: C 456 LEU cc_start: 0.9286 (tp) cc_final: 0.8705 (tp) REVERT: C 461 ASP cc_start: 0.9076 (m-30) cc_final: 0.8735 (m-30) REVERT: C 470 MET cc_start: 0.8834 (mtp) cc_final: 0.8256 (mtm) REVERT: C 476 LEU cc_start: 0.9447 (mt) cc_final: 0.9237 (mt) REVERT: C 478 SER cc_start: 0.9572 (t) cc_final: 0.9344 (p) REVERT: C 488 ARG cc_start: 0.8347 (ttp-110) cc_final: 0.7861 (tpm170) REVERT: C 492 ASP cc_start: 0.8556 (m-30) cc_final: 0.8264 (m-30) REVERT: C 500 GLU cc_start: 0.8496 (pp20) cc_final: 0.8294 (tm-30) REVERT: C 513 LYS cc_start: 0.8706 (mmmt) cc_final: 0.8358 (tppt) REVERT: D 441 GLN cc_start: 0.8097 (tp-100) cc_final: 0.7741 (tp-100) REVERT: D 453 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8001 (tm-30) REVERT: D 461 ASP cc_start: 0.8700 (m-30) cc_final: 0.8251 (t0) REVERT: D 466 ARG cc_start: 0.9037 (mpp80) cc_final: 0.8718 (mpp80) REVERT: D 474 TYR cc_start: 0.9072 (t80) cc_final: 0.8640 (t80) REVERT: D 479 THR cc_start: 0.8600 (t) cc_final: 0.8266 (t) REVERT: D 480 LYS cc_start: 0.8994 (mttp) cc_final: 0.8758 (mmmm) REVERT: D 483 ARG cc_start: 0.8668 (mtt180) cc_final: 0.8283 (ttp80) REVERT: D 507 GLN cc_start: 0.9183 (tm-30) cc_final: 0.8844 (tp-100) REVERT: E 437 GLN cc_start: 0.9379 (pt0) cc_final: 0.9164 (tt0) REVERT: E 461 ASP cc_start: 0.9003 (m-30) cc_final: 0.7759 (t70) REVERT: E 468 LEU cc_start: 0.9343 (mp) cc_final: 0.8793 (mp) REVERT: E 471 LYS cc_start: 0.8810 (tttt) cc_final: 0.8258 (pttt) REVERT: E 473 ASP cc_start: 0.8606 (m-30) cc_final: 0.8354 (m-30) REVERT: E 474 TYR cc_start: 0.9218 (t80) cc_final: 0.8918 (t80) REVERT: E 480 LYS cc_start: 0.8661 (mtpt) cc_final: 0.8302 (ttmm) REVERT: E 489 GLN cc_start: 0.8902 (mp10) cc_final: 0.8681 (mm-40) REVERT: E 503 LYS cc_start: 0.9504 (pttm) cc_final: 0.9153 (pttm) REVERT: F 445 GLU cc_start: 0.6498 (mm-30) cc_final: 0.6239 (mm-30) REVERT: F 449 ASN cc_start: 0.8139 (m-40) cc_final: 0.7856 (m-40) REVERT: G 453 GLU cc_start: 0.9032 (mp0) cc_final: 0.8689 (mp0) REVERT: G 467 ASP cc_start: 0.8633 (t70) cc_final: 0.8362 (t70) REVERT: G 470 MET cc_start: -0.0723 (ptt) cc_final: -0.1065 (ptt) REVERT: G 475 GLU cc_start: 0.7369 (mp0) cc_final: 0.6563 (pt0) REVERT: H 443 LYS cc_start: 0.9012 (mttt) cc_final: 0.8584 (mtmm) REVERT: H 470 MET cc_start: 0.8912 (mpp) cc_final: 0.8353 (mpp) REVERT: H 485 SER cc_start: 0.8533 (m) cc_final: 0.7780 (p) REVERT: H 486 LYS cc_start: 0.8360 (mtpt) cc_final: 0.8049 (mtpp) REVERT: H 488 ARG cc_start: 0.8073 (mmt90) cc_final: 0.7085 (mmt90) REVERT: H 489 GLN cc_start: 0.6963 (pm20) cc_final: 0.6372 (pm20) REVERT: H 501 PHE cc_start: 0.8215 (t80) cc_final: 0.7899 (t80) REVERT: I 445 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8184 (mp0) REVERT: I 458 GLN cc_start: 0.9260 (tp-100) cc_final: 0.9055 (tp-100) REVERT: I 479 THR cc_start: 0.8712 (m) cc_final: 0.8472 (p) REVERT: I 487 VAL cc_start: 0.8605 (t) cc_final: 0.8362 (t) REVERT: J 441 GLN cc_start: 0.7682 (tm-30) cc_final: 0.7364 (tm-30) REVERT: J 445 GLU cc_start: 0.8831 (pm20) cc_final: 0.8180 (mp0) REVERT: J 449 ASN cc_start: 0.9115 (m-40) cc_final: 0.8769 (m-40) REVERT: J 453 GLU cc_start: 0.9129 (tm-30) cc_final: 0.8374 (tm-30) REVERT: J 458 GLN cc_start: 0.9083 (tm-30) cc_final: 0.8878 (tm-30) REVERT: J 461 ASP cc_start: 0.8955 (m-30) cc_final: 0.8550 (m-30) REVERT: J 470 MET cc_start: 0.8848 (mtm) cc_final: 0.8269 (mtt) REVERT: J 476 LEU cc_start: 0.9462 (mt) cc_final: 0.9212 (mt) REVERT: J 484 THR cc_start: 0.9273 (m) cc_final: 0.8837 (m) REVERT: J 489 GLN cc_start: 0.8927 (tm-30) cc_final: 0.8612 (tm-30) REVERT: J 495 ASP cc_start: 0.9373 (m-30) cc_final: 0.9134 (m-30) REVERT: J 501 PHE cc_start: 0.9294 (t80) cc_final: 0.8805 (t80) REVERT: K 449 ASN cc_start: 0.9526 (m-40) cc_final: 0.9161 (m-40) REVERT: K 456 LEU cc_start: 0.9162 (tp) cc_final: 0.8945 (tp) REVERT: K 461 ASP cc_start: 0.8983 (t70) cc_final: 0.8547 (m-30) REVERT: K 486 LYS cc_start: 0.8628 (mtpt) cc_final: 0.8102 (mtpp) REVERT: K 503 LYS cc_start: 0.8971 (ptmm) cc_final: 0.8674 (ptmm) REVERT: L 469 ILE cc_start: 0.9136 (tt) cc_final: 0.8729 (tp) REVERT: L 486 LYS cc_start: 0.9496 (mtpp) cc_final: 0.9249 (mtpp) REVERT: L 492 ASP cc_start: 0.9300 (m-30) cc_final: 0.9054 (m-30) outliers start: 0 outliers final: 0 residues processed: 481 average time/residue: 0.2484 time to fit residues: 152.1912 Evaluate side-chains 359 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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: 4.9990 chunk 1 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 64 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN C 437 GLN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 GLN ** E 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 512 ASN F 441 GLN F 458 GLN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 ASN G 514 GLN ** H 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 449 ASN ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 449 ASN ** J 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN ** L 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 489 GLN ** L 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 1.8551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 8328 Z= 0.314 Angle : 0.803 9.096 11184 Z= 0.435 Chirality : 0.045 0.169 1332 Planarity : 0.005 0.066 1440 Dihedral : 5.489 23.082 1092 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 24.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.11 % Allowed : 2.85 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.22 (0.24), residues: 1020 helix: -0.50 (0.16), residues: 900 sheet: None (None), residues: 0 loop : -1.92 (0.50), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP K 439 PHE 0.025 0.004 PHE A 501 TYR 0.015 0.003 TYR G 474 ARG 0.010 0.001 ARG C 444 *********************** 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 453 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 452 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 ASP cc_start: 0.8996 (m-30) cc_final: 0.8649 (m-30) REVERT: A 491 LEU cc_start: 0.9603 (mm) cc_final: 0.9356 (mt) REVERT: A 492 ASP cc_start: 0.9220 (m-30) cc_final: 0.8989 (m-30) REVERT: A 500 GLU cc_start: 0.8249 (pm20) cc_final: 0.7728 (pm20) REVERT: B 441 GLN cc_start: 0.8667 (mm110) cc_final: 0.8444 (mm110) REVERT: B 480 LYS cc_start: 0.8879 (mtpp) cc_final: 0.8531 (mtpp) REVERT: B 495 ASP cc_start: 0.8105 (t70) cc_final: 0.7628 (t0) REVERT: B 503 LYS cc_start: 0.9225 (pttm) cc_final: 0.8781 (pttm) REVERT: C 446 ASP cc_start: 0.9185 (m-30) cc_final: 0.8870 (t0) REVERT: C 461 ASP cc_start: 0.8995 (m-30) cc_final: 0.8661 (m-30) REVERT: C 470 MET cc_start: 0.8702 (mtp) cc_final: 0.8406 (mtp) REVERT: C 471 LYS cc_start: 0.8645 (tmtt) cc_final: 0.8292 (tmtt) REVERT: C 477 VAL cc_start: 0.9433 (t) cc_final: 0.9175 (t) REVERT: C 478 SER cc_start: 0.9630 (t) cc_final: 0.9319 (p) REVERT: C 488 ARG cc_start: 0.8697 (ttp-110) cc_final: 0.7566 (tpm170) REVERT: C 492 ASP cc_start: 0.8788 (m-30) cc_final: 0.8073 (m-30) REVERT: C 513 LYS cc_start: 0.8822 (mmmt) cc_final: 0.8535 (tppt) REVERT: D 441 GLN cc_start: 0.8809 (tp-100) cc_final: 0.8438 (tm-30) REVERT: D 443 LYS cc_start: 0.9228 (ptmm) cc_final: 0.8453 (ptmt) REVERT: D 447 ILE cc_start: 0.9320 (mt) cc_final: 0.9106 (mm) REVERT: D 453 GLU cc_start: 0.8668 (tm-30) cc_final: 0.7817 (tm-30) REVERT: D 461 ASP cc_start: 0.8412 (m-30) cc_final: 0.8090 (t70) REVERT: D 470 MET cc_start: 0.8473 (ptp) cc_final: 0.8113 (ptt) REVERT: D 474 TYR cc_start: 0.9343 (t80) cc_final: 0.9078 (t80) REVERT: D 483 ARG cc_start: 0.8853 (mtt180) cc_final: 0.8614 (ttp80) REVERT: E 437 GLN cc_start: 0.9340 (pt0) cc_final: 0.8746 (pm20) REVERT: E 461 ASP cc_start: 0.8824 (m-30) cc_final: 0.7372 (t70) REVERT: E 471 LYS cc_start: 0.8900 (tttt) cc_final: 0.8459 (pttt) REVERT: E 480 LYS cc_start: 0.9150 (mtpt) cc_final: 0.8750 (mtpp) REVERT: E 489 GLN cc_start: 0.8932 (mp10) cc_final: 0.8566 (mp10) REVERT: F 446 ASP cc_start: 0.9024 (m-30) cc_final: 0.8784 (t0) REVERT: G 446 ASP cc_start: 0.8999 (m-30) cc_final: 0.8233 (m-30) REVERT: G 475 GLU cc_start: 0.7774 (mp0) cc_final: 0.6865 (tm-30) REVERT: G 480 LYS cc_start: 0.8651 (mmmm) cc_final: 0.8378 (mmmm) REVERT: G 500 GLU cc_start: 0.8118 (pt0) cc_final: 0.7414 (pm20) REVERT: G 515 MET cc_start: 0.3055 (mmp) cc_final: 0.2453 (mmp) REVERT: H 443 LYS cc_start: 0.9112 (mttt) cc_final: 0.8907 (mtmm) REVERT: H 461 ASP cc_start: 0.8862 (t70) cc_final: 0.8647 (t70) REVERT: H 470 MET cc_start: 0.8680 (mpp) cc_final: 0.7376 (mtm) REVERT: H 472 GLU cc_start: 0.8844 (tt0) cc_final: 0.8541 (tt0) REVERT: H 473 ASP cc_start: 0.8619 (m-30) cc_final: 0.7999 (m-30) REVERT: H 476 LEU cc_start: 0.8960 (mt) cc_final: 0.8698 (mt) REVERT: H 480 LYS cc_start: 0.8759 (mtmt) cc_final: 0.8365 (mtpt) REVERT: H 485 SER cc_start: 0.8876 (m) cc_final: 0.7862 (p) REVERT: H 489 GLN cc_start: 0.7125 (pm20) cc_final: 0.6712 (pm20) REVERT: H 500 GLU cc_start: 0.8525 (mp0) cc_final: 0.8111 (pm20) REVERT: H 501 PHE cc_start: 0.8864 (t80) cc_final: 0.8422 (t80) REVERT: H 515 MET cc_start: 0.3149 (mmp) cc_final: 0.2072 (tpp) REVERT: I 441 GLN cc_start: 0.8276 (mp10) cc_final: 0.7968 (mp10) REVERT: I 458 GLN cc_start: 0.9420 (tp-100) cc_final: 0.9217 (tp-100) REVERT: I 480 LYS cc_start: 0.9218 (mttt) cc_final: 0.8974 (mttt) REVERT: I 489 GLN cc_start: 0.8469 (tt0) cc_final: 0.7342 (tt0) REVERT: J 441 GLN cc_start: 0.7685 (tm-30) cc_final: 0.7420 (tm-30) REVERT: J 461 ASP cc_start: 0.9161 (m-30) cc_final: 0.8843 (m-30) REVERT: J 467 ASP cc_start: 0.9044 (p0) cc_final: 0.8336 (p0) REVERT: J 470 MET cc_start: 0.8878 (mtm) cc_final: 0.8274 (mtt) REVERT: J 489 GLN cc_start: 0.9158 (tm-30) cc_final: 0.8748 (tm-30) REVERT: J 495 ASP cc_start: 0.9522 (m-30) cc_final: 0.9285 (m-30) REVERT: J 501 PHE cc_start: 0.9265 (t80) cc_final: 0.8775 (t80) REVERT: K 476 LEU cc_start: 0.9178 (mt) cc_final: 0.8819 (mt) REVERT: K 486 LYS cc_start: 0.9073 (mtpt) cc_final: 0.8366 (mtpt) REVERT: K 489 GLN cc_start: 0.8986 (tm-30) cc_final: 0.8732 (tm-30) REVERT: L 442 SER cc_start: 0.9415 (t) cc_final: 0.9210 (p) REVERT: L 460 LEU cc_start: 0.9444 (mp) cc_final: 0.9192 (mp) REVERT: L 469 ILE cc_start: 0.9338 (tt) cc_final: 0.8920 (tt) REVERT: L 470 MET cc_start: 0.9248 (mpp) cc_final: 0.8039 (mtt) REVERT: L 472 GLU cc_start: 0.8596 (pt0) cc_final: 0.8178 (pm20) REVERT: L 476 LEU cc_start: 0.9510 (mt) cc_final: 0.9295 (mt) REVERT: L 480 LYS cc_start: 0.9491 (mmtp) cc_final: 0.8551 (mmmm) REVERT: L 486 LYS cc_start: 0.9468 (mtpp) cc_final: 0.9233 (mtpp) REVERT: L 489 GLN cc_start: 0.9409 (OUTLIER) cc_final: 0.9052 (mp10) REVERT: L 503 LYS cc_start: 0.9399 (mtpp) cc_final: 0.9080 (mtpp) outliers start: 1 outliers final: 0 residues processed: 452 average time/residue: 0.2219 time to fit residues: 130.6763 Evaluate side-chains 373 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 372 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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: 8.9990 chunk 18 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 77 optimal weight: 0.4980 chunk 43 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 GLN E 512 ASN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 512 ASN ** H 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 512 ASN I 449 ASN ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN ** L 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 512 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 1.9289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 8328 Z= 0.255 Angle : 0.715 7.132 11184 Z= 0.381 Chirality : 0.042 0.156 1332 Planarity : 0.004 0.067 1440 Dihedral : 5.322 23.619 1092 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 23.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.11 % Allowed : 2.43 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.25), residues: 1020 helix: -0.19 (0.17), residues: 900 sheet: None (None), residues: 0 loop : -1.95 (0.53), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 439 PHE 0.032 0.003 PHE A 501 TYR 0.011 0.002 TYR J 474 ARG 0.010 0.001 ARG K 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 460 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 459 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 ASP cc_start: 0.8993 (t70) cc_final: 0.8768 (t0) REVERT: A 461 ASP cc_start: 0.9008 (m-30) cc_final: 0.8290 (t70) REVERT: A 470 MET cc_start: 0.9036 (mtt) cc_final: 0.7872 (mtt) REVERT: A 489 GLN cc_start: 0.9116 (tp40) cc_final: 0.8727 (tp40) REVERT: A 491 LEU cc_start: 0.9607 (mm) cc_final: 0.9337 (mp) REVERT: A 492 ASP cc_start: 0.9281 (m-30) cc_final: 0.8926 (m-30) REVERT: A 500 GLU cc_start: 0.8364 (pm20) cc_final: 0.7716 (pm20) REVERT: B 445 GLU cc_start: 0.8343 (tp30) cc_final: 0.8067 (tp30) REVERT: B 472 GLU cc_start: 0.8713 (pm20) cc_final: 0.8349 (pm20) REVERT: B 473 ASP cc_start: 0.9296 (m-30) cc_final: 0.8940 (m-30) REVERT: B 495 ASP cc_start: 0.8307 (t70) cc_final: 0.7629 (t0) REVERT: C 461 ASP cc_start: 0.9108 (m-30) cc_final: 0.8713 (m-30) REVERT: C 470 MET cc_start: 0.8787 (mtp) cc_final: 0.8057 (mtp) REVERT: C 477 VAL cc_start: 0.9428 (t) cc_final: 0.9095 (t) REVERT: C 478 SER cc_start: 0.9667 (t) cc_final: 0.9379 (p) REVERT: C 488 ARG cc_start: 0.8662 (ttp-110) cc_final: 0.7542 (tpm170) REVERT: C 492 ASP cc_start: 0.8450 (m-30) cc_final: 0.7910 (m-30) REVERT: D 441 GLN cc_start: 0.8572 (tp-100) cc_final: 0.8237 (tm-30) REVERT: D 453 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8113 (tm-30) REVERT: D 461 ASP cc_start: 0.8744 (m-30) cc_final: 0.7916 (t70) REVERT: D 474 TYR cc_start: 0.9227 (t80) cc_final: 0.9024 (t80) REVERT: D 491 LEU cc_start: 0.9383 (mt) cc_final: 0.9176 (mt) REVERT: E 437 GLN cc_start: 0.9401 (pt0) cc_final: 0.8746 (tt0) REVERT: E 441 GLN cc_start: 0.9073 (mt0) cc_final: 0.8828 (mm-40) REVERT: E 458 GLN cc_start: 0.9009 (pt0) cc_final: 0.8687 (pm20) REVERT: E 461 ASP cc_start: 0.8564 (m-30) cc_final: 0.7581 (t70) REVERT: E 471 LYS cc_start: 0.8823 (tttt) cc_final: 0.8563 (pttt) REVERT: E 473 ASP cc_start: 0.8936 (m-30) cc_final: 0.8426 (m-30) REVERT: E 476 LEU cc_start: 0.9233 (mt) cc_final: 0.8227 (mt) REVERT: E 480 LYS cc_start: 0.9100 (mtpt) cc_final: 0.8673 (mtpp) REVERT: E 489 GLN cc_start: 0.8925 (mp10) cc_final: 0.8541 (mp10) REVERT: E 495 ASP cc_start: 0.9207 (m-30) cc_final: 0.9006 (m-30) REVERT: F 441 GLN cc_start: 0.8600 (tp-100) cc_final: 0.8253 (tp40) REVERT: F 446 ASP cc_start: 0.9027 (m-30) cc_final: 0.8782 (t0) REVERT: F 456 LEU cc_start: 0.9615 (tt) cc_final: 0.9255 (tt) REVERT: F 480 LYS cc_start: 0.7868 (pttt) cc_final: 0.7478 (pttm) REVERT: G 446 ASP cc_start: 0.8999 (m-30) cc_final: 0.8249 (m-30) REVERT: G 475 GLU cc_start: 0.7207 (mp0) cc_final: 0.6980 (tm-30) REVERT: G 497 GLN cc_start: 0.7654 (tp40) cc_final: 0.7280 (tp40) REVERT: G 500 GLU cc_start: 0.8457 (pt0) cc_final: 0.7762 (pm20) REVERT: G 515 MET cc_start: 0.2797 (mmp) cc_final: 0.2310 (mmp) REVERT: H 443 LYS cc_start: 0.9237 (mttt) cc_final: 0.8969 (mtmm) REVERT: H 451 MET cc_start: 0.8597 (tpp) cc_final: 0.7857 (tpp) REVERT: H 470 MET cc_start: 0.8745 (mpp) cc_final: 0.8155 (mtt) REVERT: H 476 LEU cc_start: 0.9125 (mt) cc_final: 0.8921 (mt) REVERT: H 480 LYS cc_start: 0.8828 (mtmt) cc_final: 0.8408 (mtpt) REVERT: H 485 SER cc_start: 0.8958 (m) cc_final: 0.8043 (p) REVERT: H 489 GLN cc_start: 0.7165 (pm20) cc_final: 0.6914 (pm20) REVERT: H 500 GLU cc_start: 0.8496 (mp0) cc_final: 0.8081 (pm20) REVERT: H 501 PHE cc_start: 0.8941 (t80) cc_final: 0.8232 (t80) REVERT: H 515 MET cc_start: 0.3549 (mmp) cc_final: 0.2213 (tpp) REVERT: I 459 SER cc_start: 0.9689 (m) cc_final: 0.9354 (p) REVERT: I 478 SER cc_start: 0.9475 (t) cc_final: 0.9253 (p) REVERT: I 515 MET cc_start: 0.6423 (tpt) cc_final: 0.5937 (tpp) REVERT: J 441 GLN cc_start: 0.7582 (tm-30) cc_final: 0.7300 (tm-30) REVERT: J 445 GLU cc_start: 0.9100 (pm20) cc_final: 0.8893 (pm20) REVERT: J 449 ASN cc_start: 0.9083 (m-40) cc_final: 0.8807 (m-40) REVERT: J 451 MET cc_start: 0.9367 (tpp) cc_final: 0.9060 (tpp) REVERT: J 461 ASP cc_start: 0.9155 (m-30) cc_final: 0.8755 (m-30) REVERT: J 467 ASP cc_start: 0.8877 (p0) cc_final: 0.8374 (p0) REVERT: J 470 MET cc_start: 0.8627 (mtm) cc_final: 0.7795 (mtm) REVERT: J 489 GLN cc_start: 0.9161 (tm-30) cc_final: 0.8860 (tm-30) REVERT: J 495 ASP cc_start: 0.9525 (m-30) cc_final: 0.9245 (m-30) REVERT: J 501 PHE cc_start: 0.9256 (t80) cc_final: 0.8927 (t80) REVERT: K 470 MET cc_start: 0.2911 (ptt) cc_final: 0.2601 (mtt) REVERT: K 476 LEU cc_start: 0.9317 (mt) cc_final: 0.9068 (mt) REVERT: K 486 LYS cc_start: 0.9234 (mtpt) cc_final: 0.8946 (mttm) REVERT: L 441 GLN cc_start: 0.8302 (tm-30) cc_final: 0.7879 (tm-30) REVERT: L 460 LEU cc_start: 0.9392 (mp) cc_final: 0.9180 (mp) REVERT: L 469 ILE cc_start: 0.9402 (tt) cc_final: 0.8939 (tt) REVERT: L 470 MET cc_start: 0.9317 (mpp) cc_final: 0.7848 (mtt) REVERT: L 472 GLU cc_start: 0.8558 (pt0) cc_final: 0.8347 (pm20) REVERT: L 477 VAL cc_start: 0.9344 (t) cc_final: 0.9095 (t) REVERT: L 480 LYS cc_start: 0.9477 (mmtp) cc_final: 0.8851 (mmmm) REVERT: L 486 LYS cc_start: 0.9453 (mtpp) cc_final: 0.9149 (mtmm) REVERT: L 489 GLN cc_start: 0.9390 (mm110) cc_final: 0.9144 (mm-40) REVERT: L 501 PHE cc_start: 0.9253 (t80) cc_final: 0.8968 (t80) REVERT: L 503 LYS cc_start: 0.9466 (mtpp) cc_final: 0.9164 (mtpp) outliers start: 1 outliers final: 1 residues processed: 460 average time/residue: 0.2245 time to fit residues: 134.6797 Evaluate side-chains 391 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 390 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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: 5.9990 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 57 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 GLN ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 507 GLN ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 GLN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 497 GLN H 512 ASN ** I 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 458 GLN ** J 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN K 514 GLN ** L 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 512 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 1.9586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 8328 Z= 0.214 Angle : 0.709 7.531 11184 Z= 0.375 Chirality : 0.042 0.156 1332 Planarity : 0.004 0.068 1440 Dihedral : 5.190 24.948 1092 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 22.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.11 % Allowed : 1.48 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.41 (0.26), residues: 1020 helix: 0.08 (0.17), residues: 900 sheet: None (None), residues: 0 loop : -2.02 (0.53), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 439 PHE 0.015 0.002 PHE G 501 TYR 0.023 0.002 TYR K 474 ARG 0.009 0.001 ARG J 483 *********************** 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 466 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 465 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 ASP cc_start: 0.8997 (t70) cc_final: 0.8680 (t0) REVERT: A 461 ASP cc_start: 0.8963 (m-30) cc_final: 0.8179 (t70) REVERT: A 472 GLU cc_start: 0.9062 (mp0) cc_final: 0.8702 (mp0) REVERT: A 489 GLN cc_start: 0.9085 (tp40) cc_final: 0.8672 (tp40) REVERT: A 491 LEU cc_start: 0.9602 (mm) cc_final: 0.9312 (mt) REVERT: A 492 ASP cc_start: 0.9192 (m-30) cc_final: 0.8762 (m-30) REVERT: A 500 GLU cc_start: 0.8608 (pm20) cc_final: 0.7784 (pm20) REVERT: B 441 GLN cc_start: 0.8644 (mm110) cc_final: 0.8383 (mm110) REVERT: B 445 GLU cc_start: 0.8326 (tp30) cc_final: 0.8076 (tp30) REVERT: B 470 MET cc_start: 0.8391 (mtt) cc_final: 0.8130 (mtp) REVERT: B 472 GLU cc_start: 0.8714 (pm20) cc_final: 0.7685 (pm20) REVERT: B 473 ASP cc_start: 0.9173 (m-30) cc_final: 0.8385 (m-30) REVERT: B 495 ASP cc_start: 0.8392 (t70) cc_final: 0.7745 (t0) REVERT: B 500 GLU cc_start: 0.8273 (pp20) cc_final: 0.7897 (pm20) REVERT: C 450 GLN cc_start: 0.8215 (mt0) cc_final: 0.7774 (tm-30) REVERT: C 461 ASP cc_start: 0.9121 (m-30) cc_final: 0.8755 (m-30) REVERT: C 488 ARG cc_start: 0.8757 (ttp-110) cc_final: 0.7513 (tpm170) REVERT: C 491 LEU cc_start: 0.8411 (mp) cc_final: 0.7853 (mp) REVERT: C 492 ASP cc_start: 0.8876 (m-30) cc_final: 0.8298 (m-30) REVERT: C 515 MET cc_start: 0.6774 (tpt) cc_final: 0.6554 (mmt) REVERT: D 441 GLN cc_start: 0.8502 (tp-100) cc_final: 0.8287 (tm-30) REVERT: D 449 ASN cc_start: 0.8528 (m110) cc_final: 0.8229 (m110) REVERT: D 461 ASP cc_start: 0.8442 (m-30) cc_final: 0.7657 (t70) REVERT: D 466 ARG cc_start: 0.9010 (mpp80) cc_final: 0.8767 (mpp80) REVERT: D 475 GLU cc_start: 0.9482 (tt0) cc_final: 0.9097 (tt0) REVERT: D 492 ASP cc_start: 0.9416 (p0) cc_final: 0.9186 (p0) REVERT: E 437 GLN cc_start: 0.9404 (pt0) cc_final: 0.9010 (tt0) REVERT: E 441 GLN cc_start: 0.9115 (mt0) cc_final: 0.8685 (mp10) REVERT: E 461 ASP cc_start: 0.8627 (m-30) cc_final: 0.7721 (t70) REVERT: E 471 LYS cc_start: 0.8800 (tttt) cc_final: 0.8542 (pttt) REVERT: E 476 LEU cc_start: 0.8811 (mt) cc_final: 0.8558 (mt) REVERT: E 480 LYS cc_start: 0.8954 (mtpt) cc_final: 0.8487 (mtpp) REVERT: E 489 GLN cc_start: 0.8929 (mp10) cc_final: 0.8503 (mp10) REVERT: F 441 GLN cc_start: 0.8576 (tp-100) cc_final: 0.8217 (tp40) REVERT: F 447 ILE cc_start: 0.9276 (mt) cc_final: 0.9056 (mm) REVERT: F 458 GLN cc_start: 0.9186 (pt0) cc_final: 0.8983 (pt0) REVERT: F 480 LYS cc_start: 0.8126 (pttt) cc_final: 0.7876 (pttm) REVERT: G 446 ASP cc_start: 0.8983 (m-30) cc_final: 0.8503 (m-30) REVERT: G 451 MET cc_start: 0.9142 (tpp) cc_final: 0.8906 (tpp) REVERT: G 475 GLU cc_start: 0.7309 (mp0) cc_final: 0.6979 (tm-30) REVERT: G 480 LYS cc_start: 0.8673 (mmtp) cc_final: 0.8197 (mmmm) REVERT: G 497 GLN cc_start: 0.7317 (tp40) cc_final: 0.7009 (tp-100) REVERT: G 500 GLU cc_start: 0.8192 (pt0) cc_final: 0.7476 (pm20) REVERT: G 515 MET cc_start: 0.2377 (mmp) cc_final: 0.1668 (mmp) REVERT: H 443 LYS cc_start: 0.9231 (mttt) cc_final: 0.8946 (mtmm) REVERT: H 451 MET cc_start: 0.8699 (tpp) cc_final: 0.8039 (tpp) REVERT: H 470 MET cc_start: 0.8754 (mpp) cc_final: 0.7798 (mtt) REVERT: H 473 ASP cc_start: 0.8852 (m-30) cc_final: 0.8595 (m-30) REVERT: H 476 LEU cc_start: 0.9170 (mt) cc_final: 0.8962 (mt) REVERT: H 480 LYS cc_start: 0.8797 (mtmt) cc_final: 0.8440 (mtpt) REVERT: H 485 SER cc_start: 0.8902 (m) cc_final: 0.8205 (p) REVERT: H 489 GLN cc_start: 0.7069 (pm20) cc_final: 0.6859 (pm20) REVERT: H 500 GLU cc_start: 0.8486 (mp0) cc_final: 0.8050 (pm20) REVERT: H 501 PHE cc_start: 0.8983 (t80) cc_final: 0.8168 (t80) REVERT: H 515 MET cc_start: 0.3580 (mmp) cc_final: 0.2505 (tpp) REVERT: I 459 SER cc_start: 0.9684 (m) cc_final: 0.9346 (p) REVERT: I 461 ASP cc_start: 0.9189 (m-30) cc_final: 0.8938 (m-30) REVERT: I 478 SER cc_start: 0.9481 (t) cc_final: 0.9272 (p) REVERT: I 488 ARG cc_start: 0.8478 (ptp-110) cc_final: 0.8175 (ptp-110) REVERT: I 489 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8421 (tm-30) REVERT: J 449 ASN cc_start: 0.9121 (m-40) cc_final: 0.8848 (m-40) REVERT: J 451 MET cc_start: 0.9279 (tpp) cc_final: 0.8864 (tpp) REVERT: J 461 ASP cc_start: 0.9026 (m-30) cc_final: 0.8609 (m-30) REVERT: J 467 ASP cc_start: 0.8828 (p0) cc_final: 0.8328 (p0) REVERT: J 470 MET cc_start: 0.8682 (mtm) cc_final: 0.8106 (mtm) REVERT: J 472 GLU cc_start: 0.9013 (mp0) cc_final: 0.8799 (tp30) REVERT: J 489 GLN cc_start: 0.9053 (tm-30) cc_final: 0.8771 (tm-30) REVERT: J 494 THR cc_start: 0.9482 (m) cc_final: 0.9166 (m) REVERT: J 495 ASP cc_start: 0.9525 (m-30) cc_final: 0.9229 (m-30) REVERT: J 501 PHE cc_start: 0.9065 (t80) cc_final: 0.8607 (t80) REVERT: K 445 GLU cc_start: 0.8843 (pm20) cc_final: 0.8151 (mp0) REVERT: K 461 ASP cc_start: 0.8673 (m-30) cc_final: 0.8419 (m-30) REVERT: K 471 LYS cc_start: 0.9031 (mmmm) cc_final: 0.8375 (ttpt) REVERT: K 476 LEU cc_start: 0.9340 (mt) cc_final: 0.9083 (mt) REVERT: L 437 GLN cc_start: 0.9502 (pt0) cc_final: 0.8998 (pm20) REVERT: L 441 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7662 (tm-30) REVERT: L 460 LEU cc_start: 0.9395 (mp) cc_final: 0.9169 (mp) REVERT: L 470 MET cc_start: 0.9287 (mpp) cc_final: 0.8132 (mtt) REVERT: L 472 GLU cc_start: 0.8521 (pt0) cc_final: 0.8295 (pm20) REVERT: L 476 LEU cc_start: 0.9482 (mt) cc_final: 0.9276 (mt) REVERT: L 480 LYS cc_start: 0.9483 (mmtp) cc_final: 0.8901 (mmmm) REVERT: L 486 LYS cc_start: 0.9437 (mtpp) cc_final: 0.9157 (mtmm) REVERT: L 492 ASP cc_start: 0.9273 (m-30) cc_final: 0.8666 (m-30) REVERT: L 495 ASP cc_start: 0.9551 (m-30) cc_final: 0.9130 (p0) REVERT: L 503 LYS cc_start: 0.9452 (mtpp) cc_final: 0.9154 (mtpp) outliers start: 1 outliers final: 0 residues processed: 466 average time/residue: 0.2213 time to fit residues: 135.7145 Evaluate side-chains 391 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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: 6.9990 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 8 optimal weight: 30.0000 chunk 72 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 88 optimal weight: 20.0000 chunk 80 optimal weight: 20.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** 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 458 GLN E 438 GLN E 512 ASN F 458 GLN ** 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** ** G 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 512 ASN ** I 438 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 438 GLN ** J 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 512 ASN ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN L 449 ASN ** L 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 489 GLN L 512 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 2.0623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8328 Z= 0.310 Angle : 0.799 10.041 11184 Z= 0.425 Chirality : 0.044 0.153 1332 Planarity : 0.005 0.059 1440 Dihedral : 5.456 27.720 1092 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 27.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.11 % Allowed : 2.74 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.26), residues: 1020 helix: -0.24 (0.17), residues: 900 sheet: None (None), residues: 0 loop : -2.11 (0.56), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP D 439 PHE 0.015 0.003 PHE E 501 TYR 0.014 0.002 TYR K 474 ARG 0.006 0.001 ARG J 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 455 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 454 time to evaluate : 1.123 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: A 446 ASP cc_start: 0.8987 (t70) cc_final: 0.8697 (t0) REVERT: A 461 ASP cc_start: 0.8991 (m-30) cc_final: 0.8349 (t70) REVERT: A 469 ILE cc_start: 0.8971 (tp) cc_final: 0.8733 (tt) REVERT: A 471 LYS cc_start: 0.9320 (mtmt) cc_final: 0.9007 (pttt) REVERT: A 472 GLU cc_start: 0.9077 (mp0) cc_final: 0.8876 (mp0) REVERT: A 480 LYS cc_start: 0.9157 (mmtm) cc_final: 0.8667 (mmtp) REVERT: A 491 LEU cc_start: 0.9630 (mm) cc_final: 0.9363 (mp) REVERT: A 492 ASP cc_start: 0.9239 (m-30) cc_final: 0.8792 (m-30) REVERT: A 500 GLU cc_start: 0.8539 (pm20) cc_final: 0.7746 (pm20) REVERT: B 472 GLU cc_start: 0.8650 (pm20) cc_final: 0.8242 (pm20) REVERT: B 473 ASP cc_start: 0.9128 (m-30) cc_final: 0.8849 (m-30) REVERT: B 492 ASP cc_start: 0.8930 (m-30) cc_final: 0.8477 (m-30) REVERT: B 495 ASP cc_start: 0.8601 (t70) cc_final: 0.8109 (t0) REVERT: C 450 GLN cc_start: 0.8296 (mt0) cc_final: 0.7977 (tm-30) REVERT: C 461 ASP cc_start: 0.9216 (m-30) cc_final: 0.8816 (m-30) REVERT: C 470 MET cc_start: 0.8845 (mtm) cc_final: 0.6544 (mtm) REVERT: C 471 LYS cc_start: 0.8228 (tmtt) cc_final: 0.7635 (tmtt) REVERT: C 477 VAL cc_start: 0.9481 (t) cc_final: 0.9217 (t) REVERT: C 488 ARG cc_start: 0.8878 (ttp-110) cc_final: 0.7628 (tpm170) REVERT: C 492 ASP cc_start: 0.8809 (m-30) cc_final: 0.8339 (m-30) REVERT: D 449 ASN cc_start: 0.8536 (m110) cc_final: 0.8230 (m110) REVERT: E 437 GLN cc_start: 0.9420 (pt0) cc_final: 0.8934 (tt0) REVERT: E 438 GLN cc_start: 0.9296 (OUTLIER) cc_final: 0.9026 (pp30) REVERT: E 441 GLN cc_start: 0.9102 (mt0) cc_final: 0.8841 (mt0) REVERT: E 476 LEU cc_start: 0.8801 (mt) cc_final: 0.8505 (mt) REVERT: E 480 LYS cc_start: 0.8980 (mtpt) cc_final: 0.8597 (ttmm) REVERT: E 489 GLN cc_start: 0.8909 (mp10) cc_final: 0.8484 (mp10) REVERT: F 441 GLN cc_start: 0.8770 (tp-100) cc_final: 0.8476 (tp40) REVERT: F 449 ASN cc_start: 0.8862 (m-40) cc_final: 0.8563 (m-40) REVERT: F 450 GLN cc_start: 0.8788 (tt0) cc_final: 0.7954 (pp30) REVERT: F 458 GLN cc_start: 0.9117 (pt0) cc_final: 0.8804 (pt0) REVERT: G 461 ASP cc_start: 0.8933 (m-30) cc_final: 0.8556 (m-30) REVERT: G 500 GLU cc_start: 0.8791 (pt0) cc_final: 0.8173 (pm20) REVERT: G 515 MET cc_start: 0.2971 (mmp) cc_final: 0.2143 (mmp) REVERT: H 443 LYS cc_start: 0.9297 (mttt) cc_final: 0.9079 (mtmm) REVERT: H 451 MET cc_start: 0.8719 (tpp) cc_final: 0.8148 (tpp) REVERT: H 470 MET cc_start: 0.8655 (mpp) cc_final: 0.7768 (mtt) REVERT: H 485 SER cc_start: 0.8905 (m) cc_final: 0.7821 (p) REVERT: H 486 LYS cc_start: 0.9206 (mttm) cc_final: 0.8742 (mmtm) REVERT: H 489 GLN cc_start: 0.7285 (pm20) cc_final: 0.6458 (pm20) REVERT: H 500 GLU cc_start: 0.8656 (mp0) cc_final: 0.8295 (pm20) REVERT: H 501 PHE cc_start: 0.9013 (t80) cc_final: 0.8171 (t80) REVERT: H 505 ILE cc_start: 0.9383 (mm) cc_final: 0.9147 (mm) REVERT: H 515 MET cc_start: 0.3796 (mmp) cc_final: 0.3396 (mmp) REVERT: I 458 GLN cc_start: 0.9502 (tt0) cc_final: 0.9297 (pt0) REVERT: I 459 SER cc_start: 0.9713 (m) cc_final: 0.9363 (p) REVERT: I 461 ASP cc_start: 0.9167 (m-30) cc_final: 0.8888 (m-30) REVERT: I 463 LEU cc_start: 0.9428 (mt) cc_final: 0.9224 (mt) REVERT: I 478 SER cc_start: 0.9299 (t) cc_final: 0.9064 (p) REVERT: I 488 ARG cc_start: 0.8560 (ptp-110) cc_final: 0.8281 (ptp-110) REVERT: I 491 LEU cc_start: 0.9530 (mt) cc_final: 0.9326 (mt) REVERT: I 495 ASP cc_start: 0.9279 (m-30) cc_final: 0.9072 (m-30) REVERT: J 441 GLN cc_start: 0.7928 (tm-30) cc_final: 0.7342 (tm-30) REVERT: J 449 ASN cc_start: 0.9127 (m-40) cc_final: 0.8805 (m-40) REVERT: J 453 GLU cc_start: 0.9448 (tp30) cc_final: 0.9010 (tp30) REVERT: J 458 GLN cc_start: 0.9470 (pt0) cc_final: 0.9141 (pp30) REVERT: J 467 ASP cc_start: 0.8909 (p0) cc_final: 0.8498 (p0) REVERT: J 470 MET cc_start: 0.8590 (mtm) cc_final: 0.7627 (mtm) REVERT: J 472 GLU cc_start: 0.8983 (mp0) cc_final: 0.8696 (mt-10) REVERT: J 489 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8748 (tm-30) REVERT: J 494 THR cc_start: 0.9452 (m) cc_final: 0.9179 (m) REVERT: J 495 ASP cc_start: 0.9517 (m-30) cc_final: 0.9242 (m-30) REVERT: J 501 PHE cc_start: 0.9364 (t80) cc_final: 0.9047 (t80) REVERT: K 461 ASP cc_start: 0.8834 (m-30) cc_final: 0.8474 (m-30) REVERT: K 470 MET cc_start: 0.7142 (mtm) cc_final: 0.6734 (mtt) REVERT: K 471 LYS cc_start: 0.9212 (mmmm) cc_final: 0.8790 (ttpt) REVERT: K 476 LEU cc_start: 0.9524 (mt) cc_final: 0.9318 (mt) REVERT: L 441 GLN cc_start: 0.8350 (tm-30) cc_final: 0.7698 (tm-30) REVERT: L 460 LEU cc_start: 0.9451 (mp) cc_final: 0.9228 (mp) REVERT: L 470 MET cc_start: 0.9340 (mpp) cc_final: 0.7852 (mtt) REVERT: L 472 GLU cc_start: 0.8704 (pt0) cc_final: 0.8401 (pm20) REVERT: L 476 LEU cc_start: 0.9544 (mt) cc_final: 0.9336 (mt) REVERT: L 480 LYS cc_start: 0.9375 (mmtp) cc_final: 0.8561 (mmmm) REVERT: L 486 LYS cc_start: 0.9448 (mtpp) cc_final: 0.9138 (mtmm) REVERT: L 489 GLN cc_start: 0.9429 (mm110) cc_final: 0.9071 (mp10) REVERT: L 492 ASP cc_start: 0.9174 (m-30) cc_final: 0.8818 (m-30) REVERT: L 495 ASP cc_start: 0.9514 (m-30) cc_final: 0.9229 (p0) REVERT: L 503 LYS cc_start: 0.9476 (mtpp) cc_final: 0.9087 (mtpp) outliers start: 1 outliers final: 0 residues processed: 455 average time/residue: 0.2056 time to fit residues: 124.4176 Evaluate side-chains 384 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 383 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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: 2.9990 chunk 88 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 85 optimal weight: 0.0170 chunk 56 optimal weight: 20.0000 chunk 91 optimal weight: 8.9990 overall best weight: 3.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN ** D 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 GLN E 512 ASN F 458 GLN ** 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 437 GLN H 512 ASN ** I 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 512 ASN ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 512 ASN ** L 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 458 GLN L 512 ASN L 514 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 2.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8328 Z= 0.301 Angle : 0.787 7.825 11184 Z= 0.419 Chirality : 0.046 0.183 1332 Planarity : 0.005 0.068 1440 Dihedral : 5.579 28.457 1092 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 25.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: -0.94 (0.26), residues: 1020 helix: -0.27 (0.17), residues: 900 sheet: None (None), residues: 0 loop : -2.20 (0.56), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP D 439 PHE 0.016 0.002 PHE G 501 TYR 0.019 0.003 TYR K 474 ARG 0.006 0.001 ARG J 483 *********************** 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 461 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 461 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 ASP cc_start: 0.9020 (t70) cc_final: 0.8696 (t0) REVERT: A 461 ASP cc_start: 0.8998 (m-30) cc_final: 0.8350 (t70) REVERT: A 469 ILE cc_start: 0.9050 (tp) cc_final: 0.8835 (tt) REVERT: A 470 MET cc_start: 0.9193 (mtp) cc_final: 0.8797 (mtm) REVERT: A 471 LYS cc_start: 0.9259 (mtmt) cc_final: 0.8973 (pttt) REVERT: A 472 GLU cc_start: 0.9020 (mp0) cc_final: 0.8792 (mp0) REVERT: A 489 GLN cc_start: 0.9130 (tp40) cc_final: 0.8829 (tp40) REVERT: A 491 LEU cc_start: 0.9646 (mm) cc_final: 0.9397 (mp) REVERT: A 492 ASP cc_start: 0.8973 (m-30) cc_final: 0.8700 (m-30) REVERT: B 441 GLN cc_start: 0.8188 (mm110) cc_final: 0.7303 (mm-40) REVERT: B 472 GLU cc_start: 0.8657 (pm20) cc_final: 0.8304 (pm20) REVERT: B 473 ASP cc_start: 0.9107 (m-30) cc_final: 0.8861 (m-30) REVERT: B 480 LYS cc_start: 0.9078 (mtpp) cc_final: 0.8685 (mtpp) REVERT: B 491 LEU cc_start: 0.8872 (pp) cc_final: 0.8603 (pp) REVERT: C 443 LYS cc_start: 0.9267 (pttp) cc_final: 0.9017 (ptpp) REVERT: C 444 ARG cc_start: 0.8249 (mmp-170) cc_final: 0.7726 (ttt-90) REVERT: C 470 MET cc_start: 0.8813 (mtm) cc_final: 0.7334 (mtt) REVERT: C 472 GLU cc_start: 0.9139 (mp0) cc_final: 0.8555 (mt-10) REVERT: C 488 ARG cc_start: 0.8860 (ttp-110) cc_final: 0.8461 (mtm-85) REVERT: C 492 ASP cc_start: 0.8859 (m-30) cc_final: 0.8575 (m-30) REVERT: C 503 LYS cc_start: 0.9406 (ptpp) cc_final: 0.8967 (ptpp) REVERT: C 507 GLN cc_start: 0.9252 (pp30) cc_final: 0.8605 (pp30) REVERT: D 449 ASN cc_start: 0.8723 (m110) cc_final: 0.8412 (m-40) REVERT: D 470 MET cc_start: 0.8223 (ptp) cc_final: 0.7406 (ptt) REVERT: D 473 ASP cc_start: 0.9389 (m-30) cc_final: 0.9102 (m-30) REVERT: E 437 GLN cc_start: 0.9475 (pt0) cc_final: 0.9032 (pm20) REVERT: E 441 GLN cc_start: 0.9088 (mt0) cc_final: 0.8810 (mp10) REVERT: E 458 GLN cc_start: 0.9173 (pt0) cc_final: 0.8946 (pt0) REVERT: E 461 ASP cc_start: 0.8630 (m-30) cc_final: 0.8339 (m-30) REVERT: E 476 LEU cc_start: 0.8818 (mt) cc_final: 0.8442 (mt) REVERT: E 489 GLN cc_start: 0.8784 (mp10) cc_final: 0.8542 (mp10) REVERT: E 494 THR cc_start: 0.9606 (m) cc_final: 0.9369 (m) REVERT: E 495 ASP cc_start: 0.9215 (m-30) cc_final: 0.8999 (m-30) REVERT: F 441 GLN cc_start: 0.8852 (tp-100) cc_final: 0.8631 (tp40) REVERT: F 446 ASP cc_start: 0.9225 (t70) cc_final: 0.8991 (t0) REVERT: F 447 ILE cc_start: 0.9332 (mm) cc_final: 0.9094 (mm) REVERT: F 450 GLN cc_start: 0.8551 (tt0) cc_final: 0.7999 (pp30) REVERT: F 453 GLU cc_start: 0.9138 (tm-30) cc_final: 0.8830 (tm-30) REVERT: F 458 GLN cc_start: 0.9037 (pt0) cc_final: 0.8754 (pt0) REVERT: G 461 ASP cc_start: 0.8951 (m-30) cc_final: 0.8670 (m-30) REVERT: G 467 ASP cc_start: 0.9306 (t0) cc_final: 0.9091 (t0) REVERT: G 475 GLU cc_start: 0.8454 (tp30) cc_final: 0.7729 (tm-30) REVERT: G 480 LYS cc_start: 0.9200 (mmtp) cc_final: 0.8997 (mmmm) REVERT: G 488 ARG cc_start: 0.8984 (mtt-85) cc_final: 0.8742 (mtt180) REVERT: G 489 GLN cc_start: 0.8012 (mp10) cc_final: 0.7614 (mp10) REVERT: G 500 GLU cc_start: 0.8817 (pt0) cc_final: 0.8263 (pm20) REVERT: G 515 MET cc_start: 0.2983 (mmp) cc_final: 0.2292 (mmp) REVERT: H 451 MET cc_start: 0.8801 (tpp) cc_final: 0.8242 (tpp) REVERT: H 470 MET cc_start: 0.8586 (mpp) cc_final: 0.7373 (mtm) REVERT: H 473 ASP cc_start: 0.9148 (m-30) cc_final: 0.8773 (m-30) REVERT: H 485 SER cc_start: 0.8966 (m) cc_final: 0.8189 (p) REVERT: H 489 GLN cc_start: 0.7152 (pm20) cc_final: 0.6875 (pm20) REVERT: H 492 ASP cc_start: 0.9183 (m-30) cc_final: 0.8851 (m-30) REVERT: H 494 THR cc_start: 0.9588 (m) cc_final: 0.9192 (m) REVERT: H 500 GLU cc_start: 0.8716 (mp0) cc_final: 0.8363 (pm20) REVERT: H 501 PHE cc_start: 0.8998 (t80) cc_final: 0.8052 (t80) REVERT: H 505 ILE cc_start: 0.9394 (mm) cc_final: 0.9180 (mm) REVERT: H 515 MET cc_start: 0.3764 (mmp) cc_final: 0.2820 (tpp) REVERT: I 458 GLN cc_start: 0.9458 (tt0) cc_final: 0.9237 (pt0) REVERT: I 461 ASP cc_start: 0.9094 (m-30) cc_final: 0.8818 (m-30) REVERT: I 488 ARG cc_start: 0.8770 (ptp-110) cc_final: 0.8435 (ptp-110) REVERT: J 441 GLN cc_start: 0.7689 (tm-30) cc_final: 0.7242 (tm-30) REVERT: J 449 ASN cc_start: 0.9021 (m-40) cc_final: 0.8779 (m-40) REVERT: J 453 GLU cc_start: 0.9246 (tp30) cc_final: 0.8820 (tp30) REVERT: J 467 ASP cc_start: 0.8888 (p0) cc_final: 0.8474 (p0) REVERT: J 470 MET cc_start: 0.8581 (mtm) cc_final: 0.7566 (mtm) REVERT: J 476 LEU cc_start: 0.9540 (mm) cc_final: 0.9273 (mm) REVERT: J 489 GLN cc_start: 0.9005 (tm-30) cc_final: 0.8546 (tm-30) REVERT: J 494 THR cc_start: 0.9461 (m) cc_final: 0.9120 (m) REVERT: J 495 ASP cc_start: 0.9526 (m-30) cc_final: 0.9251 (m-30) REVERT: J 501 PHE cc_start: 0.9130 (t80) cc_final: 0.8545 (t80) REVERT: K 461 ASP cc_start: 0.8790 (m-30) cc_final: 0.8424 (m-30) REVERT: L 437 GLN cc_start: 0.9341 (pt0) cc_final: 0.8709 (pm20) REVERT: L 441 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7574 (tm-30) REVERT: L 460 LEU cc_start: 0.9509 (mp) cc_final: 0.9252 (mp) REVERT: L 470 MET cc_start: 0.9173 (mpp) cc_final: 0.8636 (mtt) REVERT: L 476 LEU cc_start: 0.9570 (mt) cc_final: 0.9365 (mt) REVERT: L 480 LYS cc_start: 0.9345 (mmtp) cc_final: 0.8806 (mmmm) REVERT: L 486 LYS cc_start: 0.9444 (mtpp) cc_final: 0.9198 (mttp) REVERT: L 491 LEU cc_start: 0.9688 (mm) cc_final: 0.9453 (mp) REVERT: L 492 ASP cc_start: 0.9357 (m-30) cc_final: 0.8837 (m-30) REVERT: L 495 ASP cc_start: 0.9548 (m-30) cc_final: 0.9206 (p0) REVERT: L 503 LYS cc_start: 0.9466 (mtpp) cc_final: 0.9052 (mtpp) outliers start: 0 outliers final: 0 residues processed: 461 average time/residue: 0.2116 time to fit residues: 128.8544 Evaluate side-chains 402 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 402 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.0060 chunk 43 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 95 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 76 optimal weight: 0.5980 chunk 7 optimal weight: 0.0040 chunk 58 optimal weight: 7.9990 chunk 46 optimal weight: 0.0670 chunk 60 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 overall best weight: 0.2546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 ASN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN E 512 ASN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 449 ASN ** G 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 512 ASN I 512 ASN I 514 GLN J 512 ASN ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 458 GLN K 512 ASN K 514 GLN ** L 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 489 GLN L 512 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 2.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8328 Z= 0.235 Angle : 0.806 8.348 11184 Z= 0.417 Chirality : 0.045 0.178 1332 Planarity : 0.004 0.068 1440 Dihedral : 5.436 25.454 1092 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 24.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % 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: -0.76 (0.26), residues: 1020 helix: -0.14 (0.17), residues: 900 sheet: None (None), residues: 0 loop : -2.26 (0.57), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP D 439 PHE 0.017 0.002 PHE G 501 TYR 0.016 0.002 TYR L 474 ARG 0.012 0.001 ARG C 466 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 484 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 ASP cc_start: 0.9036 (t70) cc_final: 0.8702 (t0) REVERT: A 461 ASP cc_start: 0.8893 (m-30) cc_final: 0.8133 (t70) REVERT: A 471 LYS cc_start: 0.9246 (mtmt) cc_final: 0.8973 (pttt) REVERT: A 492 ASP cc_start: 0.8942 (m-30) cc_final: 0.8648 (m-30) REVERT: B 443 LYS cc_start: 0.8665 (ptpp) cc_final: 0.8435 (ptpp) REVERT: B 444 ARG cc_start: 0.7473 (tmm160) cc_final: 0.6868 (ttp80) REVERT: B 450 GLN cc_start: 0.7885 (tt0) cc_final: 0.7576 (tt0) REVERT: B 453 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8842 (tp30) REVERT: B 472 GLU cc_start: 0.8613 (pm20) cc_final: 0.7366 (pm20) REVERT: B 473 ASP cc_start: 0.9211 (m-30) cc_final: 0.8334 (m-30) REVERT: B 489 GLN cc_start: 0.8424 (mp10) cc_final: 0.7974 (mp10) REVERT: B 503 LYS cc_start: 0.9151 (pttm) cc_final: 0.8910 (ptpp) REVERT: C 444 ARG cc_start: 0.8361 (mmp-170) cc_final: 0.7579 (ttt-90) REVERT: C 450 GLN cc_start: 0.8395 (mt0) cc_final: 0.7946 (tm-30) REVERT: C 461 ASP cc_start: 0.9096 (m-30) cc_final: 0.8733 (m-30) REVERT: C 470 MET cc_start: 0.8891 (mtm) cc_final: 0.7118 (mtt) REVERT: C 472 GLU cc_start: 0.9086 (mp0) cc_final: 0.8501 (mt-10) REVERT: C 480 LYS cc_start: 0.8667 (ptpt) cc_final: 0.8374 (ptpp) REVERT: C 488 ARG cc_start: 0.8669 (ttp-110) cc_final: 0.8271 (mtm-85) REVERT: C 492 ASP cc_start: 0.8654 (m-30) cc_final: 0.8393 (m-30) REVERT: C 507 GLN cc_start: 0.9282 (pp30) cc_final: 0.8601 (pp30) REVERT: D 470 MET cc_start: 0.8284 (ptp) cc_final: 0.7559 (ptp) REVERT: D 497 GLN cc_start: 0.8396 (mp10) cc_final: 0.8103 (mp10) REVERT: E 437 GLN cc_start: 0.9482 (pt0) cc_final: 0.9174 (pm20) REVERT: E 441 GLN cc_start: 0.9041 (mt0) cc_final: 0.8721 (mp10) REVERT: E 452 THR cc_start: 0.8810 (p) cc_final: 0.8534 (p) REVERT: E 453 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8349 (tm-30) REVERT: E 458 GLN cc_start: 0.9168 (pt0) cc_final: 0.8941 (pt0) REVERT: E 461 ASP cc_start: 0.8677 (m-30) cc_final: 0.7946 (m-30) REVERT: E 476 LEU cc_start: 0.8652 (mt) cc_final: 0.8406 (mt) REVERT: E 489 GLN cc_start: 0.8739 (mp10) cc_final: 0.8467 (mp10) REVERT: E 494 THR cc_start: 0.9586 (m) cc_final: 0.9304 (m) REVERT: E 495 ASP cc_start: 0.9134 (m-30) cc_final: 0.8844 (m-30) REVERT: E 501 PHE cc_start: 0.9011 (t80) cc_final: 0.8347 (t80) REVERT: F 441 GLN cc_start: 0.8819 (tp-100) cc_final: 0.8513 (tm-30) REVERT: F 447 ILE cc_start: 0.9392 (mm) cc_final: 0.9098 (mm) REVERT: F 450 GLN cc_start: 0.8498 (tt0) cc_final: 0.7874 (pp30) REVERT: F 458 GLN cc_start: 0.9103 (pt0) cc_final: 0.8721 (pt0) REVERT: F 480 LYS cc_start: 0.8893 (pttt) cc_final: 0.8670 (pttm) REVERT: G 461 ASP cc_start: 0.8858 (m-30) cc_final: 0.8407 (m-30) REVERT: G 488 ARG cc_start: 0.8800 (mtt-85) cc_final: 0.8496 (mtt180) REVERT: G 500 GLU cc_start: 0.8826 (pt0) cc_final: 0.8188 (pm20) REVERT: G 515 MET cc_start: 0.2724 (mmp) cc_final: 0.2216 (mmp) REVERT: H 451 MET cc_start: 0.8863 (tpp) cc_final: 0.8414 (tpp) REVERT: H 470 MET cc_start: 0.8667 (mpp) cc_final: 0.7847 (mtt) REVERT: H 485 SER cc_start: 0.8965 (m) cc_final: 0.8141 (p) REVERT: H 500 GLU cc_start: 0.8565 (mp0) cc_final: 0.8170 (pm20) REVERT: I 459 SER cc_start: 0.9709 (m) cc_final: 0.9357 (p) REVERT: I 461 ASP cc_start: 0.9186 (m-30) cc_final: 0.8926 (m-30) REVERT: I 489 GLN cc_start: 0.8251 (tm-30) cc_final: 0.8043 (tm-30) REVERT: I 515 MET cc_start: 0.6487 (tpt) cc_final: 0.5601 (tpp) REVERT: J 441 GLN cc_start: 0.7796 (tm-30) cc_final: 0.7397 (tm-30) REVERT: J 449 ASN cc_start: 0.9059 (m-40) cc_final: 0.8768 (m-40) REVERT: J 453 GLU cc_start: 0.9257 (tp30) cc_final: 0.8688 (tp30) REVERT: J 457 ASN cc_start: 0.8560 (p0) cc_final: 0.8289 (p0) REVERT: J 461 ASP cc_start: 0.9353 (m-30) cc_final: 0.8509 (m-30) REVERT: J 467 ASP cc_start: 0.8797 (p0) cc_final: 0.8385 (p0) REVERT: J 470 MET cc_start: 0.8529 (mtm) cc_final: 0.7854 (mtm) REVERT: J 489 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8607 (tm-30) REVERT: J 494 THR cc_start: 0.9466 (m) cc_final: 0.8926 (m) REVERT: J 495 ASP cc_start: 0.9516 (m-30) cc_final: 0.9258 (m-30) REVERT: J 501 PHE cc_start: 0.8855 (t80) cc_final: 0.8289 (t80) REVERT: K 451 MET cc_start: 0.9429 (tpp) cc_final: 0.9148 (tpp) REVERT: K 458 GLN cc_start: 0.9088 (pt0) cc_final: 0.8796 (pt0) REVERT: K 461 ASP cc_start: 0.8618 (m-30) cc_final: 0.8019 (m-30) REVERT: K 499 GLU cc_start: 0.8876 (pp20) cc_final: 0.8483 (pp20) REVERT: L 437 GLN cc_start: 0.9451 (pt0) cc_final: 0.8880 (pm20) REVERT: L 441 GLN cc_start: 0.8288 (tm-30) cc_final: 0.7598 (tm-30) REVERT: L 469 ILE cc_start: 0.9374 (tt) cc_final: 0.9061 (tt) REVERT: L 470 MET cc_start: 0.9094 (mpp) cc_final: 0.8703 (mtt) REVERT: L 480 LYS cc_start: 0.9488 (mmtp) cc_final: 0.9135 (mmmm) REVERT: L 486 LYS cc_start: 0.9489 (mtpp) cc_final: 0.9247 (mtmm) REVERT: L 489 GLN cc_start: 0.9392 (mm110) cc_final: 0.8994 (mp10) REVERT: L 492 ASP cc_start: 0.9288 (m-30) cc_final: 0.8936 (m-30) REVERT: L 495 ASP cc_start: 0.9493 (m-30) cc_final: 0.9205 (p0) REVERT: L 503 LYS cc_start: 0.9467 (mtpp) cc_final: 0.9218 (mtpp) outliers start: 0 outliers final: 0 residues processed: 484 average time/residue: 0.2144 time to fit residues: 136.6317 Evaluate side-chains 416 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 416 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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: 3.9990 chunk 70 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.0050 chunk 66 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 GLN ** C 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 507 GLN E 512 ASN F 457 ASN F 458 GLN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 ASN ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 457 ASN ** H 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 512 ASN I 512 ASN J 512 ASN ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 512 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.061245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.048784 restraints weight = 40615.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.050586 restraints weight = 27086.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.051947 restraints weight = 20046.235| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 2.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8328 Z= 0.264 Angle : 0.811 8.222 11184 Z= 0.424 Chirality : 0.046 0.195 1332 Planarity : 0.005 0.068 1440 Dihedral : 5.430 26.523 1092 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 25.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % 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: -0.90 (0.26), residues: 1020 helix: -0.23 (0.17), residues: 900 sheet: None (None), residues: 0 loop : -2.32 (0.57), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP D 439 PHE 0.022 0.003 PHE A 501 TYR 0.015 0.002 TYR D 474 ARG 0.012 0.001 ARG C 466 =============================================================================== Job complete usr+sys time: 2533.79 seconds wall clock time: 46 minutes 40.42 seconds (2800.42 seconds total)