Starting phenix.real_space_refine on Thu Feb 15 08:52:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oyb_3860/02_2024/5oyb_3860.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oyb_3860/02_2024/5oyb_3860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oyb_3860/02_2024/5oyb_3860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oyb_3860/02_2024/5oyb_3860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oyb_3860/02_2024/5oyb_3860.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oyb_3860/02_2024/5oyb_3860.pdb" } resolution = 3.75 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 74 5.16 5 C 7684 2.51 5 N 1936 2.21 5 O 2072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 127": "NH1" <-> "NH2" Residue "A ARG 298": "NH1" <-> "NH2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A TYR 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 747": "NH1" <-> "NH2" Residue "B ARG 127": "NH1" <-> "NH2" Residue "B ARG 298": "NH1" <-> "NH2" Residue "B ARG 535": "NH1" <-> "NH2" Residue "B TYR 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 747": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11770 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5883 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 31, 'TRANS': 686} Chain breaks: 4 Chain: "B" Number of atoms: 5883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5883 Classifications: {'peptide': 718} Link IDs: {'PTRANS': 31, 'TRANS': 686} Chain breaks: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.63, per 1000 atoms: 0.56 Number of scatterers: 11770 At special positions: 0 Unit cell: (87.075, 125.775, 121.475, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 74 16.00 O 2072 8.00 N 1936 7.00 C 7684 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 836 " distance=2.05 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 386 " distance=2.04 Simple disulfide: pdb=" SG CYS A 625 " - pdb=" SG CYS A 630 " distance=1.97 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 836 " distance=2.05 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 386 " distance=2.04 Simple disulfide: pdb=" SG CYS B 625 " - pdb=" SG CYS B 630 " distance=1.97 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: 4.67 Conformation dependent library (CDL) restraints added in 2.3 seconds 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 62.1% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 175 through 182 removed outlier: 4.299A pdb=" N TYR A 182 " --> pdb=" O THR A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 205 through 211 Processing helix chain 'A' and resid 242 through 257 removed outlier: 3.626A pdb=" N THR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 275 removed outlier: 4.341A pdb=" N GLY A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 316 through 325 removed outlier: 3.781A pdb=" N LYS A 322 " --> pdb=" O ASP A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 359 removed outlier: 3.554A pdb=" N PHE A 332 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 343 " --> pdb=" O THR A 339 " (cutoff:3.500A) Proline residue: A 344 - end of helix removed outlier: 3.725A pdb=" N THR A 359 " --> pdb=" O TYR A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 363 removed outlier: 3.754A pdb=" N ASN A 363 " --> pdb=" O VAL A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 360 through 363' Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 395 through 405 Processing helix chain 'A' and resid 408 through 438 removed outlier: 3.553A pdb=" N TRP A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 466 Processing helix chain 'A' and resid 490 through 519 removed outlier: 3.691A pdb=" N VAL A 511 " --> pdb=" O ILE A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 569 removed outlier: 4.422A pdb=" N GLU A 555 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL A 569 " --> pdb=" O THR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 601 removed outlier: 3.877A pdb=" N LEU A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) Proline residue: A 595 - end of helix Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 630 through 644 removed outlier: 3.502A pdb=" N LEU A 634 " --> pdb=" O CYS A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 667 Proline residue: A 658 - end of helix Processing helix chain 'A' and resid 685 through 692 removed outlier: 4.082A pdb=" N ASN A 692 " --> pdb=" O GLU A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 715 removed outlier: 4.030A pdb=" N GLU A 705 " --> pdb=" O PRO A 701 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N MET A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 744 removed outlier: 3.846A pdb=" N ILE A 733 " --> pdb=" O LEU A 729 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG A 736 " --> pdb=" O ILE A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 4.277A pdb=" N ASN A 762 " --> pdb=" O GLY A 758 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N VAL A 772 " --> pdb=" O GLY A 768 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 774 " --> pdb=" O LEU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 795 removed outlier: 3.643A pdb=" N TYR A 795 " --> pdb=" O TYR A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 809 Processing helix chain 'A' and resid 854 through 885 removed outlier: 4.110A pdb=" N TRP A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP A 883 " --> pdb=" O SER A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 909 removed outlier: 3.645A pdb=" N SER A 894 " --> pdb=" O PRO A 890 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 175 through 182 removed outlier: 4.299A pdb=" N TYR B 182 " --> pdb=" O THR B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 205 through 211 Processing helix chain 'B' and resid 242 through 257 removed outlier: 3.625A pdb=" N THR B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 275 removed outlier: 4.341A pdb=" N GLY B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 305 Processing helix chain 'B' and resid 316 through 325 removed outlier: 3.781A pdb=" N LYS B 322 " --> pdb=" O ASP B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 359 removed outlier: 3.554A pdb=" N PHE B 332 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 343 " --> pdb=" O THR B 339 " (cutoff:3.500A) Proline residue: B 344 - end of helix removed outlier: 3.725A pdb=" N THR B 359 " --> pdb=" O TYR B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 363 removed outlier: 3.754A pdb=" N ASN B 363 " --> pdb=" O VAL B 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 360 through 363' Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 395 through 405 Processing helix chain 'B' and resid 408 through 438 removed outlier: 3.553A pdb=" N TRP B 438 " --> pdb=" O LEU B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 466 Processing helix chain 'B' and resid 490 through 519 removed outlier: 3.691A pdb=" N VAL B 511 " --> pdb=" O ILE B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 569 removed outlier: 4.423A pdb=" N GLU B 555 " --> pdb=" O ILE B 551 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL B 556 " --> pdb=" O LEU B 552 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL B 569 " --> pdb=" O THR B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 601 removed outlier: 3.878A pdb=" N LEU B 587 " --> pdb=" O LYS B 583 " (cutoff:3.500A) Proline residue: B 595 - end of helix Processing helix chain 'B' and resid 617 through 619 No H-bonds generated for 'chain 'B' and resid 617 through 619' Processing helix chain 'B' and resid 630 through 644 removed outlier: 3.502A pdb=" N LEU B 634 " --> pdb=" O CYS B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 667 Proline residue: B 658 - end of helix Processing helix chain 'B' and resid 685 through 692 removed outlier: 4.082A pdb=" N ASN B 692 " --> pdb=" O GLU B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 715 removed outlier: 4.030A pdb=" N GLU B 705 " --> pdb=" O PRO B 701 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N MET B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 744 removed outlier: 3.846A pdb=" N ILE B 733 " --> pdb=" O LEU B 729 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG B 736 " --> pdb=" O ILE B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 removed outlier: 4.277A pdb=" N ASN B 762 " --> pdb=" O GLY B 758 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N VAL B 772 " --> pdb=" O GLY B 768 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE B 773 " --> pdb=" O LYS B 769 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 774 " --> pdb=" O LEU B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 795 removed outlier: 3.643A pdb=" N TYR B 795 " --> pdb=" O TYR B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 809 Processing helix chain 'B' and resid 854 through 885 removed outlier: 4.110A pdb=" N TRP B 858 " --> pdb=" O SER B 854 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP B 883 " --> pdb=" O SER B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 909 removed outlier: 3.645A pdb=" N SER B 894 " --> pdb=" O PRO B 890 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 127 removed outlier: 6.762A pdb=" N PHE A 126 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 189 Processing sheet with id=AA3, first strand: chain 'A' and resid 217 through 218 Processing sheet with id=AA4, first strand: chain 'A' and resid 615 through 616 removed outlier: 4.045A pdb=" N PHE A 620 " --> pdb=" O ILE A 616 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 126 through 127 removed outlier: 6.761A pdb=" N PHE B 126 " --> pdb=" O SER B 278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 185 through 189 Processing sheet with id=AA7, first strand: chain 'B' and resid 217 through 218 Processing sheet with id=AA8, first strand: chain 'B' and resid 615 through 616 removed outlier: 4.045A pdb=" N PHE B 620 " --> pdb=" O ILE B 616 " (cutoff:3.500A) 620 hydrogen bonds defined for protein. 1842 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: 3.40 Time building geometry restraints manager: 5.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2745 1.33 - 1.45: 2648 1.45 - 1.58: 6549 1.58 - 1.70: 0 1.70 - 1.82: 122 Bond restraints: 12064 Sorted by residual: bond pdb=" CA TYR B 222 " pdb=" CB TYR B 222 " ideal model delta sigma weight residual 1.526 1.549 -0.023 9.30e-03 1.16e+04 5.86e+00 bond pdb=" CA HIS B 453 " pdb=" C HIS B 453 " ideal model delta sigma weight residual 1.525 1.553 -0.028 1.19e-02 7.06e+03 5.62e+00 bond pdb=" N LEU A 381 " pdb=" CA LEU A 381 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.15e-02 7.56e+03 5.59e+00 bond pdb=" C THR A 700 " pdb=" N PRO A 701 " ideal model delta sigma weight residual 1.337 1.363 -0.026 1.11e-02 8.12e+03 5.53e+00 bond pdb=" CA TYR A 222 " pdb=" CB TYR A 222 " ideal model delta sigma weight residual 1.526 1.548 -0.022 9.30e-03 1.16e+04 5.49e+00 ... (remaining 12059 not shown) Histogram of bond angle deviations from ideal: 96.87 - 104.33: 217 104.33 - 111.78: 4531 111.78 - 119.24: 4961 119.24 - 126.69: 6463 126.69 - 134.15: 148 Bond angle restraints: 16320 Sorted by residual: angle pdb=" N LYS B 192 " pdb=" CA LYS B 192 " pdb=" C LYS B 192 " ideal model delta sigma weight residual 110.97 116.57 -5.60 1.09e+00 8.42e-01 2.64e+01 angle pdb=" N LYS A 192 " pdb=" CA LYS A 192 " pdb=" C LYS A 192 " ideal model delta sigma weight residual 110.97 116.53 -5.56 1.09e+00 8.42e-01 2.60e+01 angle pdb=" C HIS A 453 " pdb=" N PRO A 454 " pdb=" CA PRO A 454 " ideal model delta sigma weight residual 120.04 114.85 5.19 1.08e+00 8.57e-01 2.31e+01 angle pdb=" C HIS B 453 " pdb=" N PRO B 454 " pdb=" CA PRO B 454 " ideal model delta sigma weight residual 120.04 114.85 5.19 1.08e+00 8.57e-01 2.31e+01 angle pdb=" N THR B 594 " pdb=" CA THR B 594 " pdb=" C THR B 594 " ideal model delta sigma weight residual 113.57 119.80 -6.23 1.38e+00 5.25e-01 2.04e+01 ... (remaining 16315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 6490 16.01 - 32.01: 568 32.01 - 48.01: 136 48.01 - 64.02: 14 64.02 - 80.02: 10 Dihedral angle restraints: 7218 sinusoidal: 2966 harmonic: 4252 Sorted by residual: dihedral pdb=" CB CYS A 625 " pdb=" SG CYS A 625 " pdb=" SG CYS A 630 " pdb=" CB CYS A 630 " ideal model delta sinusoidal sigma weight residual 93.00 161.75 -68.75 1 1.00e+01 1.00e-02 6.12e+01 dihedral pdb=" CB CYS B 625 " pdb=" SG CYS B 625 " pdb=" SG CYS B 630 " pdb=" CB CYS B 630 " ideal model delta sinusoidal sigma weight residual 93.00 161.74 -68.74 1 1.00e+01 1.00e-02 6.12e+01 dihedral pdb=" CB CYS A 382 " pdb=" SG CYS A 382 " pdb=" SG CYS A 386 " pdb=" CB CYS A 386 " ideal model delta sinusoidal sigma weight residual -86.00 -38.40 -47.60 1 1.00e+01 1.00e-02 3.13e+01 ... (remaining 7215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1346 0.108 - 0.217: 369 0.217 - 0.325: 63 0.325 - 0.434: 14 0.434 - 0.542: 4 Chirality restraints: 1796 Sorted by residual: chirality pdb=" CA PHE B 505 " pdb=" N PHE B 505 " pdb=" C PHE B 505 " pdb=" CB PHE B 505 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.35e+00 chirality pdb=" CA PHE A 505 " pdb=" N PHE A 505 " pdb=" C PHE A 505 " pdb=" CB PHE A 505 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.30e+00 chirality pdb=" CA THR B 594 " pdb=" N THR B 594 " pdb=" C THR B 594 " pdb=" CB THR B 594 " both_signs ideal model delta sigma weight residual False 2.53 2.03 0.50 2.00e-01 2.50e+01 6.20e+00 ... (remaining 1793 not shown) Planarity restraints: 2044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 406 " -0.045 5.00e-02 4.00e+02 6.80e-02 7.40e+00 pdb=" N PRO A 407 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 407 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 407 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 406 " 0.045 5.00e-02 4.00e+02 6.79e-02 7.38e+00 pdb=" N PRO B 407 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 407 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 407 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 222 " -0.043 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO A 223 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 223 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 223 " -0.036 5.00e-02 4.00e+02 ... (remaining 2041 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 40 2.40 - 3.02: 5734 3.02 - 3.65: 17494 3.65 - 4.27: 23937 4.27 - 4.90: 39059 Nonbonded interactions: 86264 Sorted by model distance: nonbonded pdb=" OE2 GLU B 734 " pdb="CA CA B1001 " model vdw 1.771 2.510 nonbonded pdb=" OE2 GLU A 734 " pdb="CA CA A1001 " model vdw 1.771 2.510 nonbonded pdb=" OE2 GLU A 702 " pdb="CA CA A1001 " model vdw 1.843 2.510 nonbonded pdb=" OE2 GLU B 702 " pdb="CA CA B1001 " model vdw 1.844 2.510 nonbonded pdb=" OE2 GLU A 705 " pdb="CA CA A1002 " model vdw 2.116 2.510 ... (remaining 86259 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' } 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 6.350 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 34.040 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 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 0.065 12064 Z= 0.452 Angle : 1.185 9.086 16320 Z= 0.737 Chirality : 0.104 0.542 1796 Planarity : 0.007 0.068 2044 Dihedral : 12.851 80.023 4442 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 3.12 % Allowed : 6.80 % Favored : 90.08 % Cbeta Deviations : 0.58 % 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: -3.98 (0.17), residues: 1416 helix: -2.00 (0.14), residues: 824 sheet: -2.35 (0.72), residues: 48 loop : -3.61 (0.21), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 427 HIS 0.008 0.002 HIS A 284 PHE 0.025 0.003 PHE B 585 TYR 0.018 0.003 TYR A 119 ARG 0.004 0.001 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 247 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 TYR cc_start: 0.9105 (p90) cc_final: 0.8884 (p90) REVERT: A 368 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8876 (mt-10) REVERT: A 391 MET cc_start: 0.8996 (tpt) cc_final: 0.8440 (mmm) REVERT: A 436 TYR cc_start: 0.8330 (t80) cc_final: 0.8081 (t80) REVERT: A 500 MET cc_start: 0.8523 (mtt) cc_final: 0.8209 (mtm) REVERT: A 577 GLU cc_start: 0.9055 (tp30) cc_final: 0.8846 (tt0) REVERT: A 632 MET cc_start: 0.9051 (mmp) cc_final: 0.8840 (tpp) REVERT: A 745 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8404 (tp30) REVERT: A 891 LYS cc_start: 0.8800 (tptt) cc_final: 0.8390 (ptpp) REVERT: A 900 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8259 (mt-10) REVERT: B 117 MET cc_start: 0.4586 (tmm) cc_final: 0.3647 (tpp) REVERT: B 222 TYR cc_start: 0.9114 (p90) cc_final: 0.8887 (p90) REVERT: B 368 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8844 (mt-10) REVERT: B 391 MET cc_start: 0.9019 (tpt) cc_final: 0.8473 (mmm) REVERT: B 436 TYR cc_start: 0.8355 (t80) cc_final: 0.8073 (t80) REVERT: B 500 MET cc_start: 0.8537 (mtt) cc_final: 0.8214 (mtm) REVERT: B 577 GLU cc_start: 0.9057 (tp30) cc_final: 0.8850 (tt0) REVERT: B 632 MET cc_start: 0.8992 (mmp) cc_final: 0.8790 (tpp) REVERT: B 891 LYS cc_start: 0.8810 (tptt) cc_final: 0.8391 (ptpp) REVERT: B 900 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8256 (mt-10) outliers start: 40 outliers final: 6 residues processed: 283 average time/residue: 0.2826 time to fit residues: 109.7560 Evaluate side-chains 146 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 140 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 640 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 57 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN B 183 HIS B 206 GLN ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12064 Z= 0.182 Angle : 0.655 11.288 16320 Z= 0.334 Chirality : 0.042 0.192 1796 Planarity : 0.005 0.042 2044 Dihedral : 5.623 52.320 1598 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.50 % Allowed : 11.33 % Favored : 86.17 % 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: -1.64 (0.21), residues: 1416 helix: 0.18 (0.17), residues: 842 sheet: 0.17 (0.81), residues: 28 loop : -3.31 (0.22), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 427 HIS 0.005 0.001 HIS A 849 PHE 0.039 0.001 PHE B 505 TYR 0.019 0.001 TYR A 338 ARG 0.006 0.000 ARG B 515 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 178 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LEU cc_start: 0.9195 (mt) cc_final: 0.8806 (pp) REVERT: A 176 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8407 (tpt) REVERT: A 222 TYR cc_start: 0.9116 (p90) cc_final: 0.8904 (p90) REVERT: A 368 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8809 (mp0) REVERT: A 458 TYR cc_start: 0.7452 (m-10) cc_final: 0.7184 (m-80) REVERT: A 500 MET cc_start: 0.8638 (mtt) cc_final: 0.8385 (mtm) REVERT: A 511 VAL cc_start: 0.8929 (t) cc_final: 0.8700 (m) REVERT: A 586 LEU cc_start: 0.9714 (OUTLIER) cc_final: 0.9509 (mm) REVERT: A 704 MET cc_start: 0.8962 (tpp) cc_final: 0.8537 (tpp) REVERT: A 752 ILE cc_start: 0.9144 (mm) cc_final: 0.8935 (tp) REVERT: A 880 ASP cc_start: 0.9009 (t0) cc_final: 0.8568 (m-30) REVERT: A 891 LYS cc_start: 0.8899 (tptt) cc_final: 0.8410 (pttm) REVERT: B 125 ARG cc_start: 0.8564 (tpp80) cc_final: 0.8179 (tpp80) REVERT: B 174 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8897 (pp) REVERT: B 176 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8320 (tpt) REVERT: B 199 GLN cc_start: 0.7151 (mp10) cc_final: 0.6909 (mp10) REVERT: B 222 TYR cc_start: 0.9108 (p90) cc_final: 0.8904 (p90) REVERT: B 458 TYR cc_start: 0.7431 (m-10) cc_final: 0.7162 (m-80) REVERT: B 499 PHE cc_start: 0.8337 (t80) cc_final: 0.8131 (t80) REVERT: B 500 MET cc_start: 0.8620 (mtt) cc_final: 0.8389 (mtm) REVERT: B 511 VAL cc_start: 0.9074 (t) cc_final: 0.8773 (m) REVERT: B 704 MET cc_start: 0.9002 (tpp) cc_final: 0.8580 (tpp) REVERT: B 752 ILE cc_start: 0.9155 (mm) cc_final: 0.8947 (tp) REVERT: B 880 ASP cc_start: 0.9111 (t0) cc_final: 0.8656 (m-30) REVERT: B 891 LYS cc_start: 0.8905 (tptt) cc_final: 0.8413 (pttm) outliers start: 32 outliers final: 15 residues processed: 200 average time/residue: 0.2558 time to fit residues: 72.7477 Evaluate side-chains 158 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 139 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 687 TYR Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 687 TYR Chi-restraints excluded: chain B residue 892 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 129 optimal weight: 0.5980 chunk 139 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN A 824 ASN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 ASN B 824 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12064 Z= 0.179 Angle : 0.629 10.037 16320 Z= 0.317 Chirality : 0.042 0.192 1796 Planarity : 0.004 0.035 2044 Dihedral : 5.025 47.283 1594 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.97 % Allowed : 13.36 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.22), residues: 1416 helix: 1.01 (0.18), residues: 848 sheet: 1.10 (0.78), residues: 28 loop : -3.06 (0.22), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 427 HIS 0.003 0.001 HIS A 402 PHE 0.038 0.001 PHE A 505 TYR 0.015 0.001 TYR A 687 ARG 0.007 0.000 ARG B 515 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 153 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LEU cc_start: 0.9159 (mt) cc_final: 0.8759 (pp) REVERT: A 184 ILE cc_start: 0.8967 (mt) cc_final: 0.8733 (mp) REVERT: A 186 GLU cc_start: 0.8765 (pm20) cc_final: 0.8249 (pm20) REVERT: A 368 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8848 (mt-10) REVERT: A 500 MET cc_start: 0.8648 (mtt) cc_final: 0.8393 (mtm) REVERT: A 511 VAL cc_start: 0.8969 (t) cc_final: 0.8700 (m) REVERT: A 684 LYS cc_start: 0.8610 (tppt) cc_final: 0.8194 (tptm) REVERT: A 704 MET cc_start: 0.8941 (tpp) cc_final: 0.8582 (tpp) REVERT: A 891 LYS cc_start: 0.8807 (tptt) cc_final: 0.8340 (pttm) REVERT: A 900 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8143 (mt-10) REVERT: A 907 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6145 (mp) REVERT: B 125 ARG cc_start: 0.8462 (tpp80) cc_final: 0.8243 (tpp80) REVERT: B 174 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8917 (pp) REVERT: B 186 GLU cc_start: 0.8761 (pm20) cc_final: 0.8530 (pm20) REVERT: B 199 GLN cc_start: 0.7244 (mp10) cc_final: 0.6814 (mp10) REVERT: B 500 MET cc_start: 0.8654 (mtt) cc_final: 0.8312 (mtm) REVERT: B 511 VAL cc_start: 0.9019 (t) cc_final: 0.8741 (m) REVERT: B 684 LYS cc_start: 0.8596 (tppt) cc_final: 0.8188 (tptm) REVERT: B 694 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8595 (mm-30) REVERT: B 704 MET cc_start: 0.8985 (tpp) cc_final: 0.8639 (tpp) REVERT: B 891 LYS cc_start: 0.8803 (tptt) cc_final: 0.8361 (pttm) REVERT: B 900 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8168 (mt-10) REVERT: B 907 LEU cc_start: 0.6353 (OUTLIER) cc_final: 0.6094 (mp) outliers start: 38 outliers final: 18 residues processed: 185 average time/residue: 0.2451 time to fit residues: 65.2269 Evaluate side-chains 158 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 687 TYR Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 687 TYR Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 731 ASN Chi-restraints excluded: chain B residue 892 ASP Chi-restraints excluded: chain B residue 907 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12064 Z= 0.192 Angle : 0.619 10.004 16320 Z= 0.314 Chirality : 0.042 0.209 1796 Planarity : 0.004 0.046 2044 Dihedral : 4.852 46.320 1588 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.20 % Allowed : 14.06 % Favored : 82.73 % 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: -0.20 (0.22), residues: 1416 helix: 1.32 (0.18), residues: 860 sheet: -1.01 (0.69), residues: 48 loop : -2.74 (0.24), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 427 HIS 0.005 0.001 HIS A 284 PHE 0.036 0.001 PHE A 505 TYR 0.020 0.001 TYR B 222 ARG 0.004 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 146 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ARG cc_start: 0.9183 (tpp80) cc_final: 0.8928 (tpp80) REVERT: A 174 LEU cc_start: 0.9134 (mt) cc_final: 0.8746 (pp) REVERT: A 176 MET cc_start: 0.8291 (tpt) cc_final: 0.7908 (tpt) REVERT: A 315 GLN cc_start: 0.6296 (OUTLIER) cc_final: 0.6045 (mp10) REVERT: A 368 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8871 (mt-10) REVERT: A 500 MET cc_start: 0.8585 (mtt) cc_final: 0.8308 (mtm) REVERT: A 507 ILE cc_start: 0.8306 (mt) cc_final: 0.8102 (mt) REVERT: A 511 VAL cc_start: 0.8895 (t) cc_final: 0.8644 (m) REVERT: A 704 MET cc_start: 0.9108 (tpp) cc_final: 0.8723 (tpp) REVERT: A 891 LYS cc_start: 0.8725 (tptt) cc_final: 0.8283 (pttm) REVERT: A 900 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8235 (mt-10) REVERT: B 174 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8909 (pp) REVERT: B 180 LYS cc_start: 0.9022 (mmmt) cc_final: 0.8775 (mmmt) REVERT: B 186 GLU cc_start: 0.8724 (pm20) cc_final: 0.8162 (pm20) REVERT: B 315 GLN cc_start: 0.6291 (OUTLIER) cc_final: 0.6028 (mp10) REVERT: B 500 MET cc_start: 0.8642 (mtt) cc_final: 0.8382 (mtm) REVERT: B 511 VAL cc_start: 0.9007 (t) cc_final: 0.8716 (m) REVERT: B 704 MET cc_start: 0.9101 (tpp) cc_final: 0.8712 (tpp) REVERT: B 891 LYS cc_start: 0.8733 (tptt) cc_final: 0.8309 (pttm) REVERT: B 900 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8180 (mt-10) outliers start: 41 outliers final: 28 residues processed: 177 average time/residue: 0.2524 time to fit residues: 64.6688 Evaluate side-chains 162 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 131 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 315 GLN Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 687 TYR Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 315 GLN Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 687 TYR Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 892 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 0.0070 chunk 1 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 34 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 GLN ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12064 Z= 0.160 Angle : 0.605 10.033 16320 Z= 0.303 Chirality : 0.041 0.194 1796 Planarity : 0.004 0.036 2044 Dihedral : 4.655 45.644 1588 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.97 % Allowed : 15.94 % Favored : 81.09 % 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: 0.21 (0.23), residues: 1416 helix: 1.64 (0.18), residues: 860 sheet: -0.50 (0.75), residues: 48 loop : -2.59 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 427 HIS 0.003 0.001 HIS B 402 PHE 0.030 0.001 PHE A 505 TYR 0.018 0.001 TYR A 687 ARG 0.004 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 151 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ARG cc_start: 0.9158 (tpp80) cc_final: 0.8947 (tpp80) REVERT: A 174 LEU cc_start: 0.9123 (mt) cc_final: 0.8749 (pp) REVERT: A 368 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8864 (mt-10) REVERT: A 500 MET cc_start: 0.8545 (mtt) cc_final: 0.8277 (mtm) REVERT: A 507 ILE cc_start: 0.8270 (mt) cc_final: 0.8012 (mt) REVERT: A 511 VAL cc_start: 0.8979 (t) cc_final: 0.8755 (m) REVERT: A 891 LYS cc_start: 0.8599 (tptt) cc_final: 0.8271 (pttm) REVERT: A 900 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8158 (mt-10) REVERT: A 907 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6289 (mp) REVERT: B 174 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8900 (pp) REVERT: B 176 MET cc_start: 0.8468 (tpt) cc_final: 0.8187 (tpt) REVERT: B 186 GLU cc_start: 0.8716 (pm20) cc_final: 0.8247 (pm20) REVERT: B 391 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8114 (tmm) REVERT: B 500 MET cc_start: 0.8614 (mtt) cc_final: 0.8357 (mtm) REVERT: B 511 VAL cc_start: 0.9004 (t) cc_final: 0.8779 (m) REVERT: B 684 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8422 (tptm) REVERT: B 891 LYS cc_start: 0.8660 (tptt) cc_final: 0.8310 (pttm) REVERT: B 900 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8144 (mt-10) REVERT: B 907 LEU cc_start: 0.6648 (OUTLIER) cc_final: 0.6253 (mp) outliers start: 38 outliers final: 26 residues processed: 179 average time/residue: 0.2567 time to fit residues: 66.1533 Evaluate side-chains 163 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 132 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 687 TYR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 684 LYS Chi-restraints excluded: chain B residue 687 TYR Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 892 ASP Chi-restraints excluded: chain B residue 907 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 63 optimal weight: 0.3980 chunk 11 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 132 optimal weight: 8.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12064 Z= 0.226 Angle : 0.648 10.908 16320 Z= 0.325 Chirality : 0.043 0.212 1796 Planarity : 0.004 0.040 2044 Dihedral : 4.728 45.747 1588 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.75 % Allowed : 16.64 % Favored : 79.61 % 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: 0.31 (0.23), residues: 1416 helix: 1.70 (0.18), residues: 860 sheet: -0.26 (0.75), residues: 48 loop : -2.53 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 427 HIS 0.006 0.001 HIS B 402 PHE 0.029 0.001 PHE A 505 TYR 0.014 0.001 TYR A 338 ARG 0.003 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 141 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.4499 (tmm) cc_final: 0.4171 (tpt) REVERT: A 125 ARG cc_start: 0.9139 (tpp80) cc_final: 0.8924 (tpp80) REVERT: A 174 LEU cc_start: 0.9095 (mt) cc_final: 0.8750 (pp) REVERT: A 315 GLN cc_start: 0.6430 (OUTLIER) cc_final: 0.6155 (mp10) REVERT: A 391 MET cc_start: 0.8930 (tpt) cc_final: 0.8568 (tmm) REVERT: A 500 MET cc_start: 0.8626 (mtt) cc_final: 0.8341 (mtm) REVERT: A 507 ILE cc_start: 0.8278 (mt) cc_final: 0.8073 (mt) REVERT: A 511 VAL cc_start: 0.9100 (t) cc_final: 0.8818 (m) REVERT: A 891 LYS cc_start: 0.8637 (tptt) cc_final: 0.8299 (pttm) REVERT: A 900 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8179 (mt-10) REVERT: B 174 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8915 (pp) REVERT: B 186 GLU cc_start: 0.8725 (pm20) cc_final: 0.8296 (pm20) REVERT: B 315 GLN cc_start: 0.6422 (OUTLIER) cc_final: 0.6145 (mp10) REVERT: B 391 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8206 (tmm) REVERT: B 500 MET cc_start: 0.8672 (mtt) cc_final: 0.8369 (mtm) REVERT: B 891 LYS cc_start: 0.8670 (tptt) cc_final: 0.8335 (pttm) REVERT: B 900 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8180 (mt-10) outliers start: 48 outliers final: 31 residues processed: 182 average time/residue: 0.2375 time to fit residues: 63.0349 Evaluate side-chains 161 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 126 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 315 GLN Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 687 TYR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 315 GLN Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 684 LYS Chi-restraints excluded: chain B residue 687 TYR Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 892 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 0.7980 chunk 78 optimal weight: 0.3980 chunk 100 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 136 optimal weight: 0.0980 chunk 85 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12064 Z= 0.270 Angle : 0.686 10.402 16320 Z= 0.346 Chirality : 0.044 0.198 1796 Planarity : 0.004 0.037 2044 Dihedral : 4.897 45.388 1588 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.12 % Allowed : 17.34 % Favored : 79.53 % 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: 0.26 (0.23), residues: 1416 helix: 1.65 (0.17), residues: 864 sheet: -0.10 (0.75), residues: 48 loop : -2.59 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 427 HIS 0.007 0.001 HIS A 402 PHE 0.035 0.002 PHE B 499 TYR 0.016 0.001 TYR B 338 ARG 0.003 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 138 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.4738 (tmm) cc_final: 0.4183 (tpt) REVERT: A 125 ARG cc_start: 0.9148 (tpp80) cc_final: 0.8929 (tpp80) REVERT: A 174 LEU cc_start: 0.9124 (mt) cc_final: 0.8774 (pp) REVERT: A 315 GLN cc_start: 0.6352 (OUTLIER) cc_final: 0.6052 (mp10) REVERT: A 391 MET cc_start: 0.8938 (tpt) cc_final: 0.8587 (tpp) REVERT: A 500 MET cc_start: 0.8530 (mtt) cc_final: 0.8281 (mtm) REVERT: A 511 VAL cc_start: 0.9057 (t) cc_final: 0.8820 (m) REVERT: A 891 LYS cc_start: 0.8658 (tptt) cc_final: 0.8351 (pttm) REVERT: A 900 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8203 (mt-10) REVERT: B 117 MET cc_start: 0.4553 (tmm) cc_final: 0.4004 (tpt) REVERT: B 174 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8918 (pp) REVERT: B 315 GLN cc_start: 0.6345 (OUTLIER) cc_final: 0.6041 (mp10) REVERT: B 500 MET cc_start: 0.8671 (mtt) cc_final: 0.7969 (mtm) REVERT: B 891 LYS cc_start: 0.8650 (tptt) cc_final: 0.8346 (pttm) REVERT: B 900 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8190 (mt-10) outliers start: 40 outliers final: 29 residues processed: 170 average time/residue: 0.2398 time to fit residues: 58.5192 Evaluate side-chains 158 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 126 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 315 GLN Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 687 TYR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 315 GLN Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 687 TYR Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 892 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 41 optimal weight: 0.1980 chunk 26 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 93 optimal weight: 0.0670 chunk 67 optimal weight: 0.6980 chunk 12 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12064 Z= 0.160 Angle : 0.641 9.298 16320 Z= 0.318 Chirality : 0.042 0.191 1796 Planarity : 0.004 0.038 2044 Dihedral : 4.586 44.913 1588 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.34 % Allowed : 18.12 % Favored : 79.53 % 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: 0.62 (0.23), residues: 1416 helix: 1.93 (0.18), residues: 864 sheet: 0.26 (0.76), residues: 48 loop : -2.45 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 427 HIS 0.002 0.001 HIS A 402 PHE 0.038 0.001 PHE B 505 TYR 0.015 0.001 TYR A 514 ARG 0.004 0.000 ARG B 226 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 143 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.4604 (tmm) cc_final: 0.4199 (tpt) REVERT: A 125 ARG cc_start: 0.9115 (tpp80) cc_final: 0.8896 (tpp80) REVERT: A 174 LEU cc_start: 0.9080 (mt) cc_final: 0.8744 (pp) REVERT: A 391 MET cc_start: 0.8869 (tpt) cc_final: 0.8606 (tpp) REVERT: A 500 MET cc_start: 0.8610 (mtt) cc_final: 0.8335 (mtm) REVERT: A 511 VAL cc_start: 0.9060 (t) cc_final: 0.8768 (m) REVERT: A 761 TYR cc_start: 0.8948 (t80) cc_final: 0.8596 (t80) REVERT: A 900 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8148 (mt-10) REVERT: B 117 MET cc_start: 0.4395 (tmm) cc_final: 0.4022 (tpt) REVERT: B 174 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8927 (pp) REVERT: B 500 MET cc_start: 0.8657 (mtt) cc_final: 0.8379 (mtm) REVERT: B 900 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8148 (mt-10) outliers start: 30 outliers final: 23 residues processed: 164 average time/residue: 0.2467 time to fit residues: 58.3440 Evaluate side-chains 156 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 PHE Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 687 TYR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 687 TYR Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 892 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 GLN ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 12064 Z= 0.424 Angle : 0.790 10.210 16320 Z= 0.405 Chirality : 0.048 0.231 1796 Planarity : 0.004 0.038 2044 Dihedral : 5.170 45.528 1588 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.66 % Allowed : 18.28 % Favored : 79.06 % 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: 0.12 (0.22), residues: 1416 helix: 1.58 (0.18), residues: 854 sheet: 0.15 (0.76), residues: 48 loop : -2.69 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 427 HIS 0.013 0.002 HIS A 402 PHE 0.043 0.002 PHE A 505 TYR 0.021 0.002 TYR B 338 ARG 0.006 0.001 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 132 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.4756 (tmm) cc_final: 0.4197 (tpt) REVERT: A 125 ARG cc_start: 0.9173 (tpp80) cc_final: 0.8963 (tpp80) REVERT: A 174 LEU cc_start: 0.9131 (mt) cc_final: 0.8788 (pp) REVERT: A 391 MET cc_start: 0.8922 (tpt) cc_final: 0.8548 (tpp) REVERT: A 500 MET cc_start: 0.8646 (mtt) cc_final: 0.8388 (mtm) REVERT: A 511 VAL cc_start: 0.9085 (t) cc_final: 0.8789 (m) REVERT: A 687 TYR cc_start: 0.8743 (OUTLIER) cc_final: 0.8380 (p90) REVERT: A 900 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8266 (mt-10) REVERT: B 117 MET cc_start: 0.4755 (tmm) cc_final: 0.4168 (tpt) REVERT: B 174 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8902 (pp) REVERT: B 500 MET cc_start: 0.8662 (mtt) cc_final: 0.8401 (mtm) REVERT: B 704 MET cc_start: 0.8973 (mmm) cc_final: 0.8573 (tpp) REVERT: B 900 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8252 (mt-10) outliers start: 34 outliers final: 26 residues processed: 158 average time/residue: 0.2234 time to fit residues: 52.0855 Evaluate side-chains 156 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 128 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 687 TYR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 687 TYR Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 892 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 chunk 141 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 0.0970 chunk 89 optimal weight: 0.7980 chunk 120 optimal weight: 8.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12064 Z= 0.165 Angle : 0.678 9.324 16320 Z= 0.335 Chirality : 0.042 0.212 1796 Planarity : 0.004 0.038 2044 Dihedral : 4.667 43.895 1588 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.80 % Allowed : 19.45 % Favored : 78.75 % 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: 0.64 (0.23), residues: 1416 helix: 1.96 (0.18), residues: 860 sheet: 0.44 (0.79), residues: 48 loop : -2.46 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 427 HIS 0.003 0.001 HIS A 212 PHE 0.054 0.001 PHE B 505 TYR 0.012 0.001 TYR B 514 ARG 0.002 0.000 ARG B 515 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 134 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.4635 (tmm) cc_final: 0.4299 (tpt) REVERT: A 125 ARG cc_start: 0.9118 (tpp80) cc_final: 0.8913 (tpp80) REVERT: A 174 LEU cc_start: 0.9061 (mt) cc_final: 0.8767 (pp) REVERT: A 369 MET cc_start: 0.8222 (mmt) cc_final: 0.7734 (mmm) REVERT: A 391 MET cc_start: 0.8841 (tpt) cc_final: 0.8402 (tpp) REVERT: A 500 MET cc_start: 0.8614 (mtt) cc_final: 0.8330 (mtm) REVERT: A 900 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8224 (mt-10) REVERT: A 908 PHE cc_start: 0.7982 (t80) cc_final: 0.7659 (t80) REVERT: B 117 MET cc_start: 0.4626 (tmm) cc_final: 0.4274 (tpt) REVERT: B 174 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8919 (pp) REVERT: B 500 MET cc_start: 0.8693 (mtt) cc_final: 0.8424 (mtm) REVERT: B 900 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8226 (mt-10) outliers start: 23 outliers final: 21 residues processed: 152 average time/residue: 0.2333 time to fit residues: 52.2628 Evaluate side-chains 147 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 125 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 687 TYR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 687 TYR Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 892 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 115 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.097704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.074478 restraints weight = 32119.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.076157 restraints weight = 18295.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.077189 restraints weight = 13253.683| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12064 Z= 0.233 Angle : 0.701 9.446 16320 Z= 0.349 Chirality : 0.044 0.214 1796 Planarity : 0.004 0.037 2044 Dihedral : 4.706 44.760 1588 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.27 % Allowed : 18.98 % Favored : 78.75 % 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: 0.60 (0.23), residues: 1416 helix: 1.92 (0.18), residues: 864 sheet: 0.55 (0.82), residues: 48 loop : -2.51 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 427 HIS 0.006 0.001 HIS A 402 PHE 0.047 0.002 PHE B 505 TYR 0.014 0.001 TYR A 514 ARG 0.003 0.000 ARG A 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2277.95 seconds wall clock time: 42 minutes 18.93 seconds (2538.93 seconds total)