Starting phenix.real_space_refine on Sat Dec 9 17:08:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oyb_3860/12_2023/5oyb_3860.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oyb_3860/12_2023/5oyb_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_3860/12_2023/5oyb_3860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oyb_3860/12_2023/5oyb_3860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oyb_3860/12_2023/5oyb_3860.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oyb_3860/12_2023/5oyb_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-1.21rc1-5172/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: 6.36, per 1000 atoms: 0.54 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: 4.29 Conformation dependent library (CDL) restraints added in 2.2 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: 1.16 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: 3.52 Time building geometry restraints manager: 4.69 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: 1.100 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: 6.400 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 33.460 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.100 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.870 ------------------------------------------------------------------------------- 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 : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 6 residues processed: 283 average time/residue: 0.2762 time to fit residues: 106.3585 Evaluate side-chains 138 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 132 time to evaluate : 1.549 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1148 time to fit residues: 3.2691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 59 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 57 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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 A 896 GLN B 183 HIS B 206 GLN ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 ASN B 709 GLN B 896 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12064 Z= 0.247 Angle : 0.682 10.465 16320 Z= 0.351 Chirality : 0.044 0.198 1796 Planarity : 0.005 0.057 2044 Dihedral : 5.101 20.291 1584 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.42 % Allowed : 12.42 % Favored : 85.16 % 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: -1.51 (0.21), residues: 1416 helix: 0.28 (0.17), residues: 828 sheet: 0.03 (0.82), residues: 28 loop : -3.13 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 427 HIS 0.006 0.001 HIS B 402 PHE 0.039 0.002 PHE B 505 TYR 0.021 0.002 TYR A 338 ARG 0.007 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 190 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 159 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 15 residues processed: 180 average time/residue: 0.2448 time to fit residues: 63.2593 Evaluate side-chains 144 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 1.439 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1140 time to fit residues: 4.9947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 107 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 129 optimal weight: 0.6980 chunk 139 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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 ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 ASN B 824 ASN B 896 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12064 Z= 0.252 Angle : 0.668 9.937 16320 Z= 0.342 Chirality : 0.043 0.204 1796 Planarity : 0.004 0.046 2044 Dihedral : 4.880 18.339 1584 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.50 % Allowed : 14.77 % 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: -0.81 (0.22), residues: 1416 helix: 0.88 (0.17), residues: 858 sheet: -1.70 (0.65), residues: 48 loop : -3.01 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 427 HIS 0.006 0.001 HIS B 402 PHE 0.038 0.002 PHE A 505 TYR 0.020 0.002 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 175 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 143 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 7 residues processed: 169 average time/residue: 0.2503 time to fit residues: 61.3154 Evaluate side-chains 134 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 127 time to evaluate : 1.568 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1059 time to fit residues: 3.3719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 0.0060 chunk 97 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 114 optimal weight: 0.0870 overall best weight: 0.7978 ------------------------------------------------------------------------------- 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** ** A 824 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: 0.8385 moved from start: 0.3828 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= 0.157 Angle : 0.618 9.286 16320 Z= 0.309 Chirality : 0.042 0.209 1796 Planarity : 0.004 0.043 2044 Dihedral : 4.573 19.627 1584 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.48 % Allowed : 16.33 % Favored : 82.19 % 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 (0.22), residues: 1416 helix: 1.38 (0.18), residues: 858 sheet: -1.22 (0.66), residues: 48 loop : -2.84 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 427 HIS 0.002 0.001 HIS A 402 PHE 0.036 0.001 PHE A 505 TYR 0.015 0.001 TYR A 514 ARG 0.003 0.000 ARG B 515 *********************** 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 167 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 159 average time/residue: 0.2432 time to fit residues: 55.8479 Evaluate side-chains 132 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 1.515 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1216 time to fit residues: 3.7203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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** A 431 GLN ** A 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 896 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12064 Z= 0.337 Angle : 0.714 10.427 16320 Z= 0.366 Chirality : 0.045 0.217 1796 Planarity : 0.004 0.040 2044 Dihedral : 4.830 19.530 1584 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.27 % Allowed : 18.59 % Favored : 79.14 % 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: -0.35 (0.22), residues: 1416 helix: 1.23 (0.18), residues: 854 sheet: -1.10 (0.67), residues: 48 loop : -2.80 (0.24), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 427 HIS 0.008 0.001 HIS B 402 PHE 0.028 0.002 PHE B 505 TYR 0.021 0.002 TYR B 338 ARG 0.003 0.001 ARG B 515 *********************** 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 153 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 124 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 13 residues processed: 145 average time/residue: 0.2404 time to fit residues: 51.0761 Evaluate side-chains 128 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 1.452 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1143 time to fit residues: 4.6625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 11 optimal weight: 0.0470 chunk 45 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN A 731 ASN ** A 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12064 Z= 0.152 Angle : 0.636 10.189 16320 Z= 0.314 Chirality : 0.042 0.187 1796 Planarity : 0.004 0.039 2044 Dihedral : 4.416 20.302 1584 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.56 % Allowed : 18.44 % Favored : 80.00 % 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: 0.24 (0.23), residues: 1416 helix: 1.65 (0.18), residues: 864 sheet: -0.34 (0.74), residues: 48 loop : -2.60 (0.25), 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 212 PHE 0.030 0.001 PHE A 505 TYR 0.016 0.001 TYR B 514 ARG 0.003 0.000 ARG B 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 165 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 145 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 6 residues processed: 157 average time/residue: 0.2471 time to fit residues: 56.7877 Evaluate side-chains 127 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 121 time to evaluate : 1.575 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1402 time to fit residues: 3.5274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 100 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 115 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 136 optimal weight: 0.0570 chunk 85 optimal weight: 4.9990 chunk 83 optimal weight: 0.0870 chunk 63 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 824 ASN ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12064 Z= 0.150 Angle : 0.635 9.327 16320 Z= 0.313 Chirality : 0.042 0.192 1796 Planarity : 0.004 0.037 2044 Dihedral : 4.229 19.529 1584 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.78 % Allowed : 19.61 % 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: 0.41 (0.23), residues: 1416 helix: 1.79 (0.18), residues: 866 sheet: -0.08 (0.75), residues: 48 loop : -2.60 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 427 HIS 0.002 0.001 HIS A 453 PHE 0.034 0.001 PHE B 505 TYR 0.011 0.001 TYR A 119 ARG 0.002 0.000 ARG B 515 *********************** 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 148 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 138 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 143 average time/residue: 0.2349 time to fit residues: 49.4723 Evaluate side-chains 129 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 125 time to evaluate : 1.442 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1236 time to fit residues: 2.7065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 131 optimal weight: 0.5980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.4476 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= 0.242 Angle : 0.681 9.272 16320 Z= 0.342 Chirality : 0.043 0.192 1796 Planarity : 0.004 0.037 2044 Dihedral : 4.392 18.362 1584 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.78 % Allowed : 20.00 % Favored : 79.22 % 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: 0.42 (0.23), residues: 1416 helix: 1.77 (0.18), residues: 864 sheet: 0.13 (0.75), residues: 48 loop : -2.54 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 427 HIS 0.006 0.001 HIS B 402 PHE 0.026 0.001 PHE A 505 TYR 0.014 0.001 TYR A 338 ARG 0.002 0.000 ARG A 686 *********************** 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 136 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 134 average time/residue: 0.2425 time to fit residues: 48.2991 Evaluate side-chains 122 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 119 time to evaluate : 1.523 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1202 time to fit residues: 2.6670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 131 optimal weight: 0.0670 chunk 76 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 overall best weight: 2.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12064 Z= 0.299 Angle : 0.714 9.396 16320 Z= 0.361 Chirality : 0.045 0.216 1796 Planarity : 0.004 0.037 2044 Dihedral : 4.631 19.361 1584 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.09 % Allowed : 19.14 % Favored : 79.77 % 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 (0.22), residues: 1416 helix: 1.64 (0.17), residues: 866 sheet: 0.23 (0.76), residues: 48 loop : -2.61 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 427 HIS 0.008 0.001 HIS B 402 PHE 0.039 0.002 PHE B 505 TYR 0.016 0.002 TYR B 338 ARG 0.003 0.000 ARG B 246 *********************** 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 144 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 130 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 138 average time/residue: 0.2498 time to fit residues: 50.4192 Evaluate side-chains 125 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 119 time to evaluate : 1.476 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1085 time to fit residues: 3.3592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 0.0870 chunk 63 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 11 optimal weight: 0.0470 chunk 87 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 120 optimal weight: 0.0670 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12064 Z= 0.162 Angle : 0.690 11.916 16320 Z= 0.336 Chirality : 0.042 0.198 1796 Planarity : 0.004 0.038 2044 Dihedral : 4.277 19.483 1584 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.39 % Allowed : 20.23 % Favored : 79.38 % 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: 0.65 (0.23), residues: 1416 helix: 1.90 (0.18), residues: 868 sheet: 0.75 (0.81), residues: 48 loop : -2.43 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 427 HIS 0.003 0.001 HIS A 212 PHE 0.038 0.001 PHE B 505 TYR 0.013 0.001 TYR A 514 ARG 0.004 0.000 ARG B 298 ********************** 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 141 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 136 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 137 average time/residue: 0.2417 time to fit residues: 48.7221 Evaluate side-chains 131 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 128 time to evaluate : 1.547 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1476 time to fit residues: 2.7772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 0.0020 chunk 99 optimal weight: 0.3980 chunk 6 optimal weight: 0.6980 overall best weight: 1.0192 ------------------------------------------------------------------------------- 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 709 GLN ** 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 = 0.3520 r_free = 0.3520 target = 0.099375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.076341 restraints weight = 32205.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.078053 restraints weight = 18432.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.079100 restraints weight = 13377.868| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12064 Z= 0.181 Angle : 0.691 10.849 16320 Z= 0.338 Chirality : 0.042 0.205 1796 Planarity : 0.004 0.037 2044 Dihedral : 4.216 18.899 1584 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.39 % Allowed : 20.70 % Favored : 78.91 % 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: 0.72 (0.23), residues: 1416 helix: 1.96 (0.18), residues: 864 sheet: 0.84 (0.81), residues: 48 loop : -2.36 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 427 HIS 0.004 0.001 HIS A 402 PHE 0.040 0.001 PHE B 505 TYR 0.014 0.001 TYR B 514 ARG 0.003 0.000 ARG A 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2203.90 seconds wall clock time: 40 minutes 58.02 seconds (2458.02 seconds total)