Starting phenix.real_space_refine on Thu Sep 26 02:20:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oyb_3860/09_2024/5oyb_3860.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oyb_3860/09_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_3860/09_2024/5oyb_3860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oyb_3860/09_2024/5oyb_3860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oyb_3860/09_2024/5oyb_3860.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oyb_3860/09_2024/5oyb_3860.cif" } 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. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11770 Number of models: 1 Model: "" Number of chains: 2 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: "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} Restraints were copied for chains: B Time building chain proxies: 11.81, per 1000 atoms: 1.00 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=4, 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 1.4 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: 1.26 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: 3.05 Time building geometry restraints manager: 3.17 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: 0.00 - 1.82: 14701 1.82 - 3.63: 1398 3.63 - 5.45: 161 5.45 - 7.27: 46 7.27 - 9.09: 14 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: 6487 16.01 - 32.01: 565 32.01 - 48.01: 132 48.01 - 64.02: 13 64.02 - 80.02: 9 Dihedral angle restraints: 7206 sinusoidal: 2954 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 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 dihedral pdb=" N PHE B 505 " pdb=" C PHE B 505 " pdb=" CA PHE B 505 " pdb=" CB PHE B 505 " ideal model delta harmonic sigma weight residual 122.80 135.65 -12.85 0 2.50e+00 1.60e-01 2.64e+01 ... (remaining 7203 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: 44 2.40 - 3.02: 5737 3.02 - 3.65: 17499 3.65 - 4.27: 23937 4.27 - 4.90: 39059 Nonbonded interactions: 86276 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=" SG CYS B 625 " pdb=" SG CYS B 630 " model vdw 1.971 3.760 ... (remaining 86271 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.640 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: 0.050 Extract box with map and model: 0.900 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 31.110 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 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: 38.150 ------------------------------------------------------------------------------- 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= 0.454 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 : 1.183 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: 0.2310 time to fit residues: 89.6593 Evaluate side-chains 146 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 140 time to evaluate : 1.329 ------------------------------------------------------------------------------- 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: 7.9990 chunk 107 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 57 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 128 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 296 ASN ** 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 296 ASN ** 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: 0.8345 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12064 Z= 0.173 Angle : 0.657 11.795 16320 Z= 0.334 Chirality : 0.042 0.187 1796 Planarity : 0.005 0.041 2044 Dihedral : 5.617 53.946 1598 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.19 % Allowed : 11.48 % Favored : 86.33 % 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: -1.57 (0.21), residues: 1416 helix: 0.23 (0.17), residues: 844 sheet: 0.30 (0.81), residues: 28 loop : -3.26 (0.22), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 427 HIS 0.006 0.001 HIS B 284 PHE 0.040 0.001 PHE B 505 TYR 0.018 0.001 TYR A 514 ARG 0.007 0.001 ARG A 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 208 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 180 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LEU cc_start: 0.9161 (mt) cc_final: 0.8777 (pp) REVERT: A 186 GLU cc_start: 0.8781 (pm20) cc_final: 0.8536 (pm20) REVERT: A 222 TYR cc_start: 0.9112 (p90) cc_final: 0.8892 (p90) REVERT: A 368 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8888 (mt-10) REVERT: A 458 TYR cc_start: 0.7471 (m-10) cc_final: 0.7220 (m-80) REVERT: A 500 MET cc_start: 0.8620 (mtt) cc_final: 0.8362 (mtm) REVERT: A 511 VAL cc_start: 0.8990 (t) cc_final: 0.8736 (m) REVERT: A 704 MET cc_start: 0.8959 (tpp) cc_final: 0.8627 (tpp) REVERT: A 752 ILE cc_start: 0.9151 (mm) cc_final: 0.8944 (tp) REVERT: A 880 ASP cc_start: 0.9012 (t0) cc_final: 0.8579 (m-30) REVERT: A 891 LYS cc_start: 0.8855 (tptt) cc_final: 0.8398 (pttm) REVERT: B 125 ARG cc_start: 0.8651 (tpp80) cc_final: 0.8268 (tpp80) REVERT: B 174 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8910 (pp) REVERT: B 176 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8155 (tpt) REVERT: B 186 GLU cc_start: 0.8733 (pm20) cc_final: 0.8511 (pm20) REVERT: B 199 GLN cc_start: 0.7146 (mp10) cc_final: 0.6881 (mp10) REVERT: B 222 TYR cc_start: 0.9104 (p90) cc_final: 0.8901 (p90) REVERT: B 458 TYR cc_start: 0.7416 (m-10) cc_final: 0.7171 (m-80) REVERT: B 500 MET cc_start: 0.8600 (mtt) cc_final: 0.8364 (mtm) REVERT: B 511 VAL cc_start: 0.9033 (t) cc_final: 0.8729 (m) REVERT: B 704 MET cc_start: 0.8945 (tpp) cc_final: 0.8616 (tpp) REVERT: B 752 ILE cc_start: 0.9135 (mm) cc_final: 0.8924 (tp) REVERT: B 880 ASP cc_start: 0.9093 (t0) cc_final: 0.8649 (m-30) REVERT: B 891 LYS cc_start: 0.8895 (tptt) cc_final: 0.8408 (pttm) outliers start: 28 outliers final: 10 residues processed: 200 average time/residue: 0.2299 time to fit residues: 64.6352 Evaluate side-chains 151 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 VAL 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 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 107 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 129 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 chunk 115 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3270 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= 0.190 Angle : 0.640 10.340 16320 Z= 0.323 Chirality : 0.042 0.194 1796 Planarity : 0.004 0.035 2044 Dihedral : 5.028 47.442 1591 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.42 % Allowed : 13.44 % Favored : 84.14 % 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: -0.62 (0.22), residues: 1416 helix: 1.04 (0.18), residues: 848 sheet: 0.95 (0.78), residues: 28 loop : -3.01 (0.22), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 427 HIS 0.004 0.001 HIS B 284 PHE 0.038 0.001 PHE A 505 TYR 0.017 0.001 TYR A 687 ARG 0.009 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 181 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 150 time to evaluate : 2.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LEU cc_start: 0.9150 (mt) cc_final: 0.8766 (pp) REVERT: A 186 GLU cc_start: 0.8741 (pm20) cc_final: 0.8226 (pm20) REVERT: A 341 MET cc_start: 0.9309 (tpp) cc_final: 0.9050 (tpp) REVERT: A 368 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8860 (mt-10) REVERT: A 500 MET cc_start: 0.8634 (mtt) cc_final: 0.8380 (mtm) REVERT: A 511 VAL cc_start: 0.9034 (t) cc_final: 0.8749 (m) REVERT: A 704 MET cc_start: 0.9003 (tpp) cc_final: 0.8645 (tpp) REVERT: A 891 LYS cc_start: 0.8828 (tptt) cc_final: 0.8371 (pttm) REVERT: A 900 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8132 (mt-10) REVERT: A 907 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6142 (mp) REVERT: B 125 ARG cc_start: 0.8718 (tpp80) cc_final: 0.8343 (tpp80) REVERT: B 174 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8937 (pp) REVERT: B 186 GLU cc_start: 0.8731 (pm20) cc_final: 0.8487 (pm20) REVERT: B 199 GLN cc_start: 0.7395 (mp10) cc_final: 0.6950 (mp10) REVERT: B 341 MET cc_start: 0.9309 (tpp) cc_final: 0.9050 (tpp) REVERT: B 500 MET cc_start: 0.8657 (mtt) cc_final: 0.8392 (mtm) REVERT: B 511 VAL cc_start: 0.9045 (t) cc_final: 0.8766 (m) REVERT: B 624 GLU cc_start: 0.8812 (tp30) cc_final: 0.8570 (tp30) REVERT: B 694 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8693 (mm-30) REVERT: B 704 MET cc_start: 0.9016 (tpp) cc_final: 0.8663 (tpp) REVERT: B 891 LYS cc_start: 0.8849 (tptt) cc_final: 0.8382 (pttm) REVERT: B 900 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8152 (mt-10) REVERT: B 907 LEU cc_start: 0.6350 (OUTLIER) cc_final: 0.6087 (mp) outliers start: 31 outliers final: 15 residues processed: 177 average time/residue: 0.2568 time to fit residues: 65.4589 Evaluate side-chains 156 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 276 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 714 THR 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 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 907 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 0.0970 chunk 97 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 129 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 114 optimal weight: 0.4980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12064 Z= 0.147 Angle : 0.603 9.928 16320 Z= 0.303 Chirality : 0.041 0.197 1796 Planarity : 0.004 0.046 2044 Dihedral : 4.737 47.299 1588 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.34 % Allowed : 13.91 % Favored : 83.75 % 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: -0.11 (0.22), residues: 1416 helix: 1.41 (0.18), residues: 858 sheet: -1.01 (0.72), residues: 48 loop : -2.72 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 427 HIS 0.003 0.001 HIS B 284 PHE 0.036 0.001 PHE B 505 TYR 0.022 0.001 TYR B 222 ARG 0.005 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 179 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 149 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LEU cc_start: 0.9154 (mt) cc_final: 0.8802 (pp) REVERT: A 176 MET cc_start: 0.8504 (tpt) cc_final: 0.8228 (tpt) REVERT: A 341 MET cc_start: 0.9312 (tpp) cc_final: 0.9089 (tpp) REVERT: A 368 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8827 (mt-10) REVERT: A 369 MET cc_start: 0.8266 (mtm) cc_final: 0.7998 (tpp) REVERT: A 391 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.7627 (tmm) REVERT: A 511 VAL cc_start: 0.8978 (t) cc_final: 0.8711 (m) REVERT: A 624 GLU cc_start: 0.8755 (tp30) cc_final: 0.8490 (tp30) REVERT: A 891 LYS cc_start: 0.8701 (tptt) cc_final: 0.8289 (pttm) REVERT: A 900 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8220 (mt-10) REVERT: B 174 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8910 (pp) REVERT: B 341 MET cc_start: 0.9305 (tpp) cc_final: 0.9084 (tpp) REVERT: B 391 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8292 (tmm) REVERT: B 500 MET cc_start: 0.8654 (mtt) cc_final: 0.8351 (mtm) REVERT: B 511 VAL cc_start: 0.9025 (t) cc_final: 0.8753 (m) REVERT: B 624 GLU cc_start: 0.8911 (tp30) cc_final: 0.8665 (tp30) REVERT: B 891 LYS cc_start: 0.8725 (tptt) cc_final: 0.8323 (pttm) REVERT: B 900 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8172 (mt-10) outliers start: 30 outliers final: 17 residues processed: 171 average time/residue: 0.2326 time to fit residues: 57.7754 Evaluate side-chains 156 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 391 MET 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 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 272 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 391 MET 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 794 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.7892 > 50: distance: 2 - 18: 8.726 distance: 6 - 23: 14.106 distance: 13 - 18: 6.308 distance: 18 - 19: 11.554 distance: 19 - 20: 12.236 distance: 19 - 22: 12.485 distance: 20 - 21: 10.191 distance: 20 - 23: 19.751 distance: 23 - 24: 13.797 distance: 24 - 25: 3.929 distance: 24 - 27: 12.659 distance: 25 - 26: 10.884 distance: 25 - 32: 29.609 distance: 27 - 28: 21.577 distance: 28 - 29: 9.390 distance: 29 - 30: 11.542 distance: 32 - 33: 13.649 distance: 33 - 34: 33.712 distance: 33 - 36: 28.248 distance: 34 - 35: 36.501 distance: 34 - 42: 10.282 distance: 36 - 37: 15.274 distance: 37 - 38: 27.647 distance: 37 - 39: 34.778 distance: 38 - 40: 15.748 distance: 39 - 41: 13.140 distance: 40 - 41: 13.912 distance: 42 - 43: 9.161 distance: 43 - 44: 28.032 distance: 43 - 46: 39.199 distance: 44 - 45: 32.287 distance: 44 - 53: 21.805 distance: 46 - 47: 45.386 distance: 47 - 48: 37.086 distance: 49 - 50: 17.458 distance: 50 - 51: 22.255 distance: 50 - 52: 19.259 distance: 53 - 54: 18.910 distance: 53 - 59: 17.358 distance: 54 - 55: 27.468 distance: 54 - 57: 28.096 distance: 55 - 56: 23.087 distance: 57 - 58: 19.511 distance: 58 - 59: 24.588 distance: 60 - 61: 17.372 distance: 61 - 62: 10.353 distance: 61 - 64: 22.030 distance: 62 - 63: 52.323 distance: 62 - 69: 8.017 distance: 64 - 65: 41.060 distance: 65 - 66: 13.996 distance: 66 - 67: 24.254 distance: 66 - 68: 13.551 distance: 69 - 70: 10.346 distance: 70 - 71: 33.310 distance: 70 - 73: 28.203 distance: 71 - 72: 30.011 distance: 71 - 76: 18.025 distance: 73 - 74: 10.847 distance: 73 - 75: 41.685 distance: 76 - 77: 13.223 distance: 76 - 134: 27.532 distance: 77 - 78: 27.827 distance: 77 - 80: 15.570 distance: 78 - 79: 14.775 distance: 78 - 83: 9.884 distance: 79 - 131: 14.097 distance: 80 - 81: 16.356 distance: 80 - 82: 3.040 distance: 83 - 84: 10.155 distance: 84 - 85: 8.454 distance: 84 - 87: 10.208 distance: 85 - 86: 15.142 distance: 85 - 92: 15.697 distance: 87 - 88: 18.833 distance: 88 - 89: 5.262 distance: 89 - 90: 13.733 distance: 90 - 91: 7.597 distance: 92 - 93: 8.513 distance: 93 - 94: 7.944 distance: 93 - 96: 7.785 distance: 94 - 95: 9.255 distance: 94 - 103: 14.040 distance: 96 - 97: 6.904 distance: 97 - 98: 5.384 distance: 98 - 99: 10.880 distance: 99 - 100: 3.754 distance: 100 - 102: 3.329