Starting phenix.real_space_refine on Tue May 13 23:34:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j7a_61199/05_2025/9j7a_61199.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j7a_61199/05_2025/9j7a_61199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j7a_61199/05_2025/9j7a_61199.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j7a_61199/05_2025/9j7a_61199.map" model { file = "/net/cci-nas-00/data/ceres_data/9j7a_61199/05_2025/9j7a_61199.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j7a_61199/05_2025/9j7a_61199.cif" } resolution = 4.13 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 6939 2.51 5 N 1954 2.21 5 O 2081 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11036 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4932 Classifications: {'peptide': 627} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Chain: "B" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 572 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 6, 'TRANS': 66} Chain: "C" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 490 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 5, 'TRANS': 56} Chain: "F" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 55 Classifications: {'peptide': 11} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'TRANS': 10} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'UNK:plan-1': 11} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 4932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4932 Classifications: {'peptide': 627} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Chain: "E" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 55 Classifications: {'peptide': 11} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'TRANS': 10} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'UNK:plan-1': 11} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 10.85, per 1000 atoms: 0.98 Number of scatterers: 11036 At special positions: 0 Unit cell: (116.44, 127.1, 158.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 2081 8.00 N 1954 7.00 C 6939 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.5 seconds 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2678 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 1 sheets defined 71.6% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 1 through 14 Processing helix chain 'A' and resid 16 through 23 Processing helix chain 'A' and resid 28 through 37 Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 48 through 57 removed outlier: 3.851A pdb=" N GLY A 57 " --> pdb=" O ALA A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 67 Processing helix chain 'A' and resid 90 through 99 Processing helix chain 'A' and resid 100 through 111 removed outlier: 3.641A pdb=" N GLY A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 133 through 143 Processing helix chain 'A' and resid 156 through 164 removed outlier: 3.558A pdb=" N LYS A 164 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 199 through 209 Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 231 through 240 Processing helix chain 'A' and resid 245 through 262 removed outlier: 3.614A pdb=" N ARG A 249 " --> pdb=" O ASP A 245 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 284 Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 310 through 317 Processing helix chain 'A' and resid 320 through 337 Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 343 through 357 removed outlier: 4.382A pdb=" N ILE A 347 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR A 349 " --> pdb=" O HIS A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 377 removed outlier: 3.531A pdb=" N CYS A 363 " --> pdb=" O GLU A 359 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 398 Processing helix chain 'A' and resid 403 through 428 Processing helix chain 'A' and resid 432 through 456 Processing helix chain 'A' and resid 461 through 478 Processing helix chain 'A' and resid 486 through 493 Processing helix chain 'A' and resid 501 through 506 Processing helix chain 'A' and resid 511 through 521 Processing helix chain 'A' and resid 534 through 540 Processing helix chain 'A' and resid 545 through 547 No H-bonds generated for 'chain 'A' and resid 545 through 547' Processing helix chain 'A' and resid 548 through 562 Processing helix chain 'A' and resid 582 through 593 Processing helix chain 'A' and resid 596 through 608 removed outlier: 4.399A pdb=" N ALA A 602 " --> pdb=" O LYS A 598 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA A 607 " --> pdb=" O ARG A 603 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 627 Processing helix chain 'B' and resid 63 through 84 removed outlier: 3.682A pdb=" N GLN B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE B 70 " --> pdb=" O VAL B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 101 removed outlier: 3.677A pdb=" N GLY B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY B 101 " --> pdb=" O ILE B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 110 removed outlier: 3.609A pdb=" N GLN B 108 " --> pdb=" O GLN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 115 through 125 Processing helix chain 'C' and resid 68 through 83 removed outlier: 3.585A pdb=" N ILE C 74 " --> pdb=" O PHE C 70 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU C 81 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 100 removed outlier: 3.926A pdb=" N ASN C 95 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA C 96 " --> pdb=" O HIS C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 114 removed outlier: 4.181A pdb=" N GLN C 108 " --> pdb=" O GLN C 104 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 109 " --> pdb=" O GLN C 105 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN C 112 " --> pdb=" O GLN C 108 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 126 removed outlier: 3.618A pdb=" N MET C 121 " --> pdb=" O PRO C 117 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS C 125 " --> pdb=" O MET C 121 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 11 removed outlier: 3.665A pdb=" N UNK F 9 " --> pdb=" O UNK F 5 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N UNK F 10 " --> pdb=" O UNK F 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 14 Processing helix chain 'D' and resid 16 through 26 removed outlier: 4.043A pdb=" N LEU D 20 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASN D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 36 Processing helix chain 'D' and resid 48 through 57 Processing helix chain 'D' and resid 58 through 69 removed outlier: 3.796A pdb=" N VAL D 62 " --> pdb=" O HIS D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 99 Processing helix chain 'D' and resid 100 through 111 removed outlier: 3.512A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 132 Processing helix chain 'D' and resid 133 through 143 Processing helix chain 'D' and resid 156 through 164 removed outlier: 3.504A pdb=" N ILE D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 176 Processing helix chain 'D' and resid 189 through 198 Processing helix chain 'D' and resid 199 through 209 Processing helix chain 'D' and resid 221 through 229 Processing helix chain 'D' and resid 231 through 240 removed outlier: 4.053A pdb=" N VAL D 235 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 262 removed outlier: 3.552A pdb=" N GLU D 251 " --> pdb=" O ARG D 247 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN D 262 " --> pdb=" O ALA D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 285 Processing helix chain 'D' and resid 299 through 303 removed outlier: 3.540A pdb=" N GLY D 303 " --> pdb=" O HIS D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 317 removed outlier: 4.035A pdb=" N LEU D 314 " --> pdb=" O ASN D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 337 Processing helix chain 'D' and resid 344 through 357 Processing helix chain 'D' and resid 359 through 377 Processing helix chain 'D' and resid 381 through 398 removed outlier: 3.567A pdb=" N LEU D 385 " --> pdb=" O THR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 428 Processing helix chain 'D' and resid 432 through 457 Processing helix chain 'D' and resid 460 through 478 Processing helix chain 'D' and resid 486 through 493 Processing helix chain 'D' and resid 502 through 507 removed outlier: 3.849A pdb=" N VAL D 506 " --> pdb=" O HIS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 522 Processing helix chain 'D' and resid 534 through 541 removed outlier: 3.666A pdb=" N ILE D 539 " --> pdb=" O ALA D 535 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN D 541 " --> pdb=" O HIS D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 563 Processing helix chain 'D' and resid 582 through 593 removed outlier: 3.665A pdb=" N GLU D 586 " --> pdb=" O THR D 582 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 608 removed outlier: 3.610A pdb=" N ARG D 606 " --> pdb=" O ALA D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 627 removed outlier: 3.672A pdb=" N HIS D 627 " --> pdb=" O PHE D 623 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 10 Processing sheet with id=AA1, first strand: chain 'D' and resid 77 through 81 removed outlier: 6.260A pdb=" N GLY D 77 " --> pdb=" O GLY D 88 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY D 88 " --> pdb=" O GLY D 77 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL D 79 " --> pdb=" O ILE D 86 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1863 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.91 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3769 1.34 - 1.46: 2077 1.46 - 1.58: 5291 1.58 - 1.70: 0 1.70 - 1.81: 88 Bond restraints: 11225 Sorted by residual: bond pdb=" C PRO B 116 " pdb=" N PRO B 117 " ideal model delta sigma weight residual 1.335 1.353 -0.019 1.28e-02 6.10e+03 2.10e+00 bond pdb=" C PRO C 116 " pdb=" N PRO C 117 " ideal model delta sigma weight residual 1.335 1.350 -0.014 1.36e-02 5.41e+03 1.14e+00 bond pdb=" N ARG A 80 " pdb=" CA ARG A 80 " ideal model delta sigma weight residual 1.462 1.477 -0.015 1.54e-02 4.22e+03 9.01e-01 bond pdb=" CA THR B 113 " pdb=" C THR B 113 " ideal model delta sigma weight residual 1.522 1.536 -0.014 1.52e-02 4.33e+03 8.93e-01 bond pdb=" CG LEU A 519 " pdb=" CD2 LEU A 519 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.31e-01 ... (remaining 11220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 14976 2.15 - 4.29: 193 4.29 - 6.44: 43 6.44 - 8.59: 10 8.59 - 10.74: 2 Bond angle restraints: 15224 Sorted by residual: angle pdb=" N SER A 40 " pdb=" CA SER A 40 " pdb=" C SER A 40 " ideal model delta sigma weight residual 111.90 117.23 -5.33 1.32e+00 5.74e-01 1.63e+01 angle pdb=" N ARG D 309 " pdb=" CA ARG D 309 " pdb=" C ARG D 309 " ideal model delta sigma weight residual 114.56 109.46 5.10 1.27e+00 6.20e-01 1.61e+01 angle pdb=" C LEU A 65 " pdb=" N LEU A 66 " pdb=" CA LEU A 66 " ideal model delta sigma weight residual 121.98 116.76 5.22 1.53e+00 4.27e-01 1.16e+01 angle pdb=" N PRO B 116 " pdb=" CA PRO B 116 " pdb=" C PRO B 116 " ideal model delta sigma weight residual 110.70 114.49 -3.79 1.22e+00 6.72e-01 9.66e+00 angle pdb=" CA LEU A 519 " pdb=" CB LEU A 519 " pdb=" CG LEU A 519 " ideal model delta sigma weight residual 116.30 127.04 -10.74 3.50e+00 8.16e-02 9.41e+00 ... (remaining 15219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 6045 17.14 - 34.27: 594 34.27 - 51.41: 128 51.41 - 68.55: 25 68.55 - 85.68: 14 Dihedral angle restraints: 6806 sinusoidal: 2675 harmonic: 4131 Sorted by residual: dihedral pdb=" CA VAL A 39 " pdb=" C VAL A 39 " pdb=" N SER A 40 " pdb=" CA SER A 40 " ideal model delta harmonic sigma weight residual 180.00 156.69 23.31 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA LYS A 598 " pdb=" C LYS A 598 " pdb=" N CYS A 599 " pdb=" CA CYS A 599 " ideal model delta harmonic sigma weight residual 180.00 161.64 18.36 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CG ARG D 55 " pdb=" CD ARG D 55 " pdb=" NE ARG D 55 " pdb=" CZ ARG D 55 " ideal model delta sinusoidal sigma weight residual -180.00 -137.55 -42.45 2 1.50e+01 4.44e-03 9.72e+00 ... (remaining 6803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1283 0.041 - 0.082: 384 0.082 - 0.123: 78 0.123 - 0.163: 18 0.163 - 0.204: 4 Chirality restraints: 1767 Sorted by residual: chirality pdb=" CB VAL A 492 " pdb=" CA VAL A 492 " pdb=" CG1 VAL A 492 " pdb=" CG2 VAL A 492 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA LEU A 66 " pdb=" N LEU A 66 " pdb=" C LEU A 66 " pdb=" CB LEU A 66 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA ILE D 616 " pdb=" N ILE D 616 " pdb=" C ILE D 616 " pdb=" CB ILE D 616 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.52e-01 ... (remaining 1764 not shown) Planarity restraints: 1983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 48 " 0.049 5.00e-02 4.00e+02 7.36e-02 8.66e+00 pdb=" N PRO A 49 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 49 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 49 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 616 " -0.048 5.00e-02 4.00e+02 7.23e-02 8.37e+00 pdb=" N PRO D 617 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO D 617 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 617 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 404 " -0.042 5.00e-02 4.00e+02 6.39e-02 6.54e+00 pdb=" N PRO D 405 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 405 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 405 " -0.036 5.00e-02 4.00e+02 ... (remaining 1980 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 2260 2.78 - 3.31: 11763 3.31 - 3.84: 19246 3.84 - 4.37: 21902 4.37 - 4.90: 35475 Nonbonded interactions: 90646 Sorted by model distance: nonbonded pdb=" OG SER A 580 " pdb=" OG SER A 585 " model vdw 2.244 3.040 nonbonded pdb=" OG SER A 40 " pdb=" OE1 GLN A 42 " model vdw 2.258 3.040 nonbonded pdb=" O THR A 73 " pdb=" OG1 THR A 90 " model vdw 2.283 3.040 nonbonded pdb=" OH TYR A 449 " pdb=" O PRO A 497 " model vdw 2.285 3.040 nonbonded pdb=" NH2 ARG D 332 " pdb=" OD2 ASP D 342 " model vdw 2.299 3.120 ... (remaining 90641 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 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 13.490 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: 0.500 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 30.970 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 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 : 0.003 0.033 11225 Z= 0.143 Angle : 0.663 10.736 15224 Z= 0.342 Chirality : 0.042 0.204 1767 Planarity : 0.005 0.074 1983 Dihedral : 14.848 85.683 4128 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.08 % Allowed : 0.76 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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 (0.21), residues: 1381 helix: -0.02 (0.16), residues: 901 sheet: None (None), residues: 0 loop : -1.38 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 367 HIS 0.005 0.001 HIS A 537 PHE 0.021 0.001 PHE A 388 TYR 0.018 0.001 TYR D 542 ARG 0.005 0.000 ARG A 379 Details of bonding type rmsd hydrogen bonds : bond 0.19823 ( 630) hydrogen bonds : angle 6.55585 ( 1863) covalent geometry : bond 0.00305 (11225) covalent geometry : angle 0.66323 (15224) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 348 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8750 (t80) cc_final: 0.8482 (t80) REVERT: A 41 GLN cc_start: 0.8809 (pp30) cc_final: 0.8514 (pp30) REVERT: A 58 HIS cc_start: 0.7541 (m90) cc_final: 0.7239 (m90) REVERT: A 60 LYS cc_start: 0.8997 (mmmm) cc_final: 0.8683 (mtpp) REVERT: A 75 GLN cc_start: 0.7011 (mp10) cc_final: 0.6723 (mp10) REVERT: A 100 HIS cc_start: 0.6061 (m-70) cc_final: 0.5823 (m-70) REVERT: A 131 ASP cc_start: 0.9119 (t70) cc_final: 0.8837 (t0) REVERT: A 133 ARG cc_start: 0.8529 (mmm-85) cc_final: 0.8044 (mmm-85) REVERT: A 175 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8442 (mt-10) REVERT: A 205 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8830 (tp30) REVERT: A 231 LYS cc_start: 0.8579 (mmtp) cc_final: 0.8317 (mmtm) REVERT: A 239 LEU cc_start: 0.9261 (tt) cc_final: 0.8961 (mt) REVERT: A 356 ASP cc_start: 0.8958 (m-30) cc_final: 0.8072 (t70) REVERT: A 395 MET cc_start: 0.8677 (ttm) cc_final: 0.8445 (ttm) REVERT: A 397 HIS cc_start: 0.8001 (t-170) cc_final: 0.7770 (t70) REVERT: A 483 GLU cc_start: 0.9157 (mp0) cc_final: 0.8921 (mp0) REVERT: A 507 CYS cc_start: 0.7624 (m) cc_final: 0.7268 (m) REVERT: A 541 GLN cc_start: 0.8608 (mt0) cc_final: 0.7559 (tm-30) REVERT: A 567 ASP cc_start: 0.7813 (t70) cc_final: 0.7540 (t70) REVERT: A 574 LYS cc_start: 0.9199 (mttp) cc_final: 0.8871 (mtmt) REVERT: B 70 PHE cc_start: 0.7663 (t80) cc_final: 0.7461 (t80) REVERT: B 76 LEU cc_start: 0.9110 (mp) cc_final: 0.8730 (mp) REVERT: B 92 HIS cc_start: 0.8378 (m90) cc_final: 0.7407 (m90) REVERT: B 118 VAL cc_start: 0.8706 (t) cc_final: 0.8482 (t) REVERT: C 76 LEU cc_start: 0.7938 (mt) cc_final: 0.7417 (mt) REVERT: D 105 LYS cc_start: 0.9348 (pttp) cc_final: 0.9132 (pttt) REVERT: D 147 ILE cc_start: 0.8170 (pt) cc_final: 0.7858 (mm) REVERT: D 173 LEU cc_start: 0.9106 (tp) cc_final: 0.8529 (tp) REVERT: D 228 GLU cc_start: 0.8225 (tt0) cc_final: 0.7908 (tt0) REVERT: D 273 TYR cc_start: 0.8149 (t80) cc_final: 0.7561 (t80) REVERT: D 274 HIS cc_start: 0.8173 (m90) cc_final: 0.7731 (m90) REVERT: D 321 ARG cc_start: 0.8326 (ptt180) cc_final: 0.7989 (ptm-80) REVERT: D 322 ASP cc_start: 0.9082 (p0) cc_final: 0.8694 (p0) REVERT: D 394 GLN cc_start: 0.9178 (tt0) cc_final: 0.8632 (tp40) REVERT: D 572 GLN cc_start: 0.9006 (mp10) cc_final: 0.8784 (mp10) REVERT: D 621 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8027 (mm-30) outliers start: 1 outliers final: 0 residues processed: 348 average time/residue: 0.2312 time to fit residues: 113.1533 Evaluate side-chains 234 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 58 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 GLN D 380 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.133455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.108465 restraints weight = 34972.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.109956 restraints weight = 20864.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.110616 restraints weight = 15121.949| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11225 Z= 0.196 Angle : 0.661 11.546 15224 Z= 0.342 Chirality : 0.041 0.215 1767 Planarity : 0.005 0.063 1983 Dihedral : 4.506 20.755 1523 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.25 % Allowed : 5.79 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.01 (0.23), residues: 1381 helix: 0.65 (0.16), residues: 941 sheet: None (None), residues: 0 loop : -1.34 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 209 HIS 0.008 0.001 HIS D 325 PHE 0.022 0.002 PHE A 388 TYR 0.016 0.001 TYR A 445 ARG 0.007 0.001 ARG A 171 Details of bonding type rmsd hydrogen bonds : bond 0.04892 ( 630) hydrogen bonds : angle 5.03563 ( 1863) covalent geometry : bond 0.00424 (11225) covalent geometry : angle 0.66119 (15224) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 280 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LEU cc_start: 0.8750 (mt) cc_final: 0.8333 (mt) REVERT: A 41 GLN cc_start: 0.8669 (pp30) cc_final: 0.8421 (pp30) REVERT: A 55 ARG cc_start: 0.8974 (tpp-160) cc_final: 0.8704 (tpp80) REVERT: A 58 HIS cc_start: 0.7759 (m90) cc_final: 0.7228 (m-70) REVERT: A 60 LYS cc_start: 0.9046 (mmmm) cc_final: 0.8788 (mtpp) REVERT: A 75 GLN cc_start: 0.6777 (mp10) cc_final: 0.6564 (mp10) REVERT: A 131 ASP cc_start: 0.9033 (t70) cc_final: 0.8814 (t0) REVERT: A 133 ARG cc_start: 0.8502 (mmm-85) cc_final: 0.8268 (mmm-85) REVERT: A 175 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8528 (mt-10) REVERT: A 239 LEU cc_start: 0.9182 (tt) cc_final: 0.8977 (mt) REVERT: A 422 MET cc_start: 0.8206 (ttm) cc_final: 0.7915 (ttt) REVERT: A 507 CYS cc_start: 0.7913 (m) cc_final: 0.7506 (m) REVERT: A 541 GLN cc_start: 0.8547 (mt0) cc_final: 0.7397 (tm-30) REVERT: A 561 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8214 (tm-30) REVERT: A 567 ASP cc_start: 0.7579 (t70) cc_final: 0.7366 (t0) REVERT: A 579 LYS cc_start: 0.7377 (mttm) cc_final: 0.7118 (mttt) REVERT: A 620 LEU cc_start: 0.8624 (mm) cc_final: 0.8324 (mm) REVERT: B 92 HIS cc_start: 0.8660 (m90) cc_final: 0.7930 (m90) REVERT: B 118 VAL cc_start: 0.9065 (t) cc_final: 0.8765 (t) REVERT: C 76 LEU cc_start: 0.8217 (mt) cc_final: 0.7871 (mt) REVERT: C 92 HIS cc_start: 0.8931 (t70) cc_final: 0.8598 (t70) REVERT: D 147 ILE cc_start: 0.8418 (pt) cc_final: 0.8058 (mm) REVERT: D 271 LYS cc_start: 0.9158 (mmtt) cc_final: 0.8958 (mmpt) REVERT: D 273 TYR cc_start: 0.8120 (t80) cc_final: 0.7782 (t80) REVERT: D 321 ARG cc_start: 0.8451 (ptt180) cc_final: 0.8214 (ptt90) REVERT: D 340 ASN cc_start: 0.8724 (t0) cc_final: 0.8439 (t0) REVERT: D 394 GLN cc_start: 0.9266 (tt0) cc_final: 0.8834 (tp40) REVERT: D 538 ILE cc_start: 0.9606 (mt) cc_final: 0.9397 (tp) REVERT: D 621 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8010 (mm-30) outliers start: 3 outliers final: 1 residues processed: 280 average time/residue: 0.2375 time to fit residues: 93.5075 Evaluate side-chains 227 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 62 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 86 optimal weight: 0.0970 chunk 112 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 HIS ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.132770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.109202 restraints weight = 36011.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.110876 restraints weight = 20086.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.111434 restraints weight = 14118.002| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11225 Z= 0.139 Angle : 0.604 9.132 15224 Z= 0.313 Chirality : 0.040 0.181 1767 Planarity : 0.005 0.061 1983 Dihedral : 4.421 21.406 1523 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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 (0.23), residues: 1381 helix: 0.81 (0.17), residues: 938 sheet: None (None), residues: 0 loop : -1.47 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 209 HIS 0.009 0.001 HIS D 372 PHE 0.023 0.001 PHE A 549 TYR 0.013 0.001 TYR D 472 ARG 0.008 0.000 ARG D 264 Details of bonding type rmsd hydrogen bonds : bond 0.04300 ( 630) hydrogen bonds : angle 4.72744 ( 1863) covalent geometry : bond 0.00301 (11225) covalent geometry : angle 0.60429 (15224) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LEU cc_start: 0.8750 (mt) cc_final: 0.8344 (mt) REVERT: A 41 GLN cc_start: 0.8582 (pp30) cc_final: 0.8342 (pp30) REVERT: A 58 HIS cc_start: 0.7801 (m90) cc_final: 0.7321 (m-70) REVERT: A 60 LYS cc_start: 0.9039 (mmmm) cc_final: 0.8682 (mtpp) REVERT: A 138 LYS cc_start: 0.9342 (tppp) cc_final: 0.8987 (tppt) REVERT: A 171 ARG cc_start: 0.8303 (ptp90) cc_final: 0.7713 (ptp90) REVERT: A 231 LYS cc_start: 0.8875 (mmtp) cc_final: 0.8506 (mmtm) REVERT: A 268 ASP cc_start: 0.8365 (t0) cc_final: 0.8110 (t0) REVERT: A 439 ASN cc_start: 0.8157 (t0) cc_final: 0.7913 (t0) REVERT: A 507 CYS cc_start: 0.7977 (m) cc_final: 0.7552 (m) REVERT: A 515 THR cc_start: 0.9508 (p) cc_final: 0.9299 (t) REVERT: A 541 GLN cc_start: 0.8405 (mt0) cc_final: 0.7466 (tm-30) REVERT: A 561 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8169 (tm-30) REVERT: A 567 ASP cc_start: 0.7417 (t70) cc_final: 0.7142 (t0) REVERT: A 620 LEU cc_start: 0.8606 (mm) cc_final: 0.8266 (mm) REVERT: B 91 ASP cc_start: 0.8802 (t70) cc_final: 0.8583 (t70) REVERT: B 92 HIS cc_start: 0.8710 (m90) cc_final: 0.7901 (m90) REVERT: B 118 VAL cc_start: 0.9026 (t) cc_final: 0.8681 (t) REVERT: C 76 LEU cc_start: 0.8164 (mt) cc_final: 0.7781 (mt) REVERT: C 92 HIS cc_start: 0.8869 (t70) cc_final: 0.8615 (t70) REVERT: D 135 ASP cc_start: 0.9149 (p0) cc_final: 0.8883 (p0) REVERT: D 147 ILE cc_start: 0.8401 (pt) cc_final: 0.8052 (mm) REVERT: D 273 TYR cc_start: 0.8067 (t80) cc_final: 0.7742 (t80) REVERT: D 319 GLN cc_start: 0.7766 (pm20) cc_final: 0.7548 (pm20) REVERT: D 340 ASN cc_start: 0.8523 (t0) cc_final: 0.8236 (t0) REVERT: D 394 GLN cc_start: 0.9228 (tt0) cc_final: 0.8829 (tp40) REVERT: D 538 ILE cc_start: 0.9602 (mt) cc_final: 0.9388 (tp) REVERT: D 621 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7810 (mm-30) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.2212 time to fit residues: 85.3210 Evaluate side-chains 220 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 49 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 130 optimal weight: 0.4980 chunk 53 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 60 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 553 HIS D 155 ASN D 380 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.121943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.098145 restraints weight = 35622.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.099373 restraints weight = 20789.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.099962 restraints weight = 14898.170| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11225 Z= 0.134 Angle : 0.600 9.083 15224 Z= 0.309 Chirality : 0.039 0.180 1767 Planarity : 0.004 0.060 1983 Dihedral : 4.391 20.863 1523 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.23), residues: 1381 helix: 0.95 (0.17), residues: 940 sheet: None (None), residues: 0 loop : -1.47 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 209 HIS 0.008 0.001 HIS D 372 PHE 0.022 0.002 PHE A 549 TYR 0.014 0.001 TYR D 267 ARG 0.006 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.03965 ( 630) hydrogen bonds : angle 4.61228 ( 1863) covalent geometry : bond 0.00295 (11225) covalent geometry : angle 0.59981 (15224) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LEU cc_start: 0.8719 (mt) cc_final: 0.8312 (mt) REVERT: A 34 TYR cc_start: 0.8615 (t80) cc_final: 0.7940 (t80) REVERT: A 41 GLN cc_start: 0.8557 (pp30) cc_final: 0.8334 (pp30) REVERT: A 58 HIS cc_start: 0.7758 (m90) cc_final: 0.7294 (m-70) REVERT: A 60 LYS cc_start: 0.9062 (mmmm) cc_final: 0.8696 (mtpp) REVERT: A 133 ARG cc_start: 0.8495 (mmm-85) cc_final: 0.8285 (mmm-85) REVERT: A 138 LYS cc_start: 0.9389 (tppp) cc_final: 0.9164 (tppt) REVERT: A 176 GLN cc_start: 0.7835 (mm110) cc_final: 0.7184 (mp10) REVERT: A 231 LYS cc_start: 0.8911 (mmtp) cc_final: 0.8673 (mmtm) REVERT: A 507 CYS cc_start: 0.7928 (m) cc_final: 0.7479 (m) REVERT: A 541 GLN cc_start: 0.8309 (mt0) cc_final: 0.7351 (tm-30) REVERT: A 561 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8200 (tm-30) REVERT: A 567 ASP cc_start: 0.7376 (t70) cc_final: 0.7143 (t0) REVERT: A 620 LEU cc_start: 0.8601 (mm) cc_final: 0.8253 (mm) REVERT: B 70 PHE cc_start: 0.8692 (t80) cc_final: 0.8491 (t80) REVERT: B 76 LEU cc_start: 0.9193 (mt) cc_final: 0.8986 (mt) REVERT: B 92 HIS cc_start: 0.8671 (m90) cc_final: 0.7854 (m90) REVERT: B 118 VAL cc_start: 0.9035 (t) cc_final: 0.8708 (t) REVERT: C 76 LEU cc_start: 0.8151 (mt) cc_final: 0.7781 (mt) REVERT: D 135 ASP cc_start: 0.9077 (p0) cc_final: 0.8812 (p0) REVERT: D 147 ILE cc_start: 0.8409 (pt) cc_final: 0.8058 (mm) REVERT: D 273 TYR cc_start: 0.8142 (t80) cc_final: 0.7745 (t80) REVERT: D 394 GLN cc_start: 0.9285 (tt0) cc_final: 0.8868 (tp40) REVERT: D 538 ILE cc_start: 0.9594 (mt) cc_final: 0.9376 (tp) REVERT: D 568 MET cc_start: 0.8121 (ptt) cc_final: 0.7916 (ptp) REVERT: D 621 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7815 (mm-30) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.2186 time to fit residues: 88.1354 Evaluate side-chains 218 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 90 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 95 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS A 166 HIS ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 ASN D 443 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.132671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.108853 restraints weight = 34857.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.109258 restraints weight = 20805.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.110191 restraints weight = 15998.823| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11225 Z= 0.147 Angle : 0.614 9.222 15224 Z= 0.316 Chirality : 0.040 0.239 1767 Planarity : 0.005 0.060 1983 Dihedral : 4.395 22.263 1523 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.34 (0.23), residues: 1381 helix: 1.00 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -1.39 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 209 HIS 0.008 0.001 HIS D 274 PHE 0.015 0.001 PHE A 623 TYR 0.016 0.001 TYR D 267 ARG 0.005 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.03850 ( 630) hydrogen bonds : angle 4.60970 ( 1863) covalent geometry : bond 0.00327 (11225) covalent geometry : angle 0.61422 (15224) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 LEU cc_start: 0.8728 (mt) cc_final: 0.8329 (mt) REVERT: A 34 TYR cc_start: 0.8645 (t80) cc_final: 0.7867 (t80) REVERT: A 58 HIS cc_start: 0.7777 (m90) cc_final: 0.7283 (m-70) REVERT: A 60 LYS cc_start: 0.9044 (mmmm) cc_final: 0.8739 (mmmm) REVERT: A 86 ILE cc_start: 0.7980 (mm) cc_final: 0.7751 (mm) REVERT: A 507 CYS cc_start: 0.7816 (m) cc_final: 0.7405 (m) REVERT: A 541 GLN cc_start: 0.8290 (mt0) cc_final: 0.7256 (tm-30) REVERT: A 561 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8166 (tm-30) REVERT: A 620 LEU cc_start: 0.8608 (mm) cc_final: 0.8267 (mm) REVERT: B 70 PHE cc_start: 0.8678 (t80) cc_final: 0.8410 (t80) REVERT: B 118 VAL cc_start: 0.9018 (t) cc_final: 0.8678 (t) REVERT: C 76 LEU cc_start: 0.8197 (mt) cc_final: 0.7832 (mt) REVERT: D 1 MET cc_start: 0.1863 (mpp) cc_final: 0.1488 (mpp) REVERT: D 135 ASP cc_start: 0.9174 (p0) cc_final: 0.8847 (p0) REVERT: D 147 ILE cc_start: 0.8468 (pt) cc_final: 0.8141 (mm) REVERT: D 196 GLU cc_start: 0.8697 (tt0) cc_final: 0.8382 (pt0) REVERT: D 260 PHE cc_start: 0.8931 (m-80) cc_final: 0.8622 (m-80) REVERT: D 273 TYR cc_start: 0.8064 (t80) cc_final: 0.7689 (t80) REVERT: D 280 MET cc_start: 0.7768 (tpp) cc_final: 0.7445 (tpt) REVERT: D 394 GLN cc_start: 0.9273 (tt0) cc_final: 0.8835 (tp40) REVERT: D 417 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7827 (tm-30) REVERT: D 538 ILE cc_start: 0.9587 (mt) cc_final: 0.9362 (tp) REVERT: D 586 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7607 (tt0) REVERT: D 621 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7775 (mm-30) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.2158 time to fit residues: 87.3815 Evaluate side-chains 216 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.3537 > 50: distance: 40 - 66: 25.914 distance: 45 - 52: 17.604 distance: 46 - 74: 31.999 distance: 52 - 53: 49.895 distance: 53 - 54: 41.865 distance: 53 - 56: 32.056 distance: 54 - 55: 11.125 distance: 54 - 58: 47.016 distance: 55 - 85: 34.039 distance: 56 - 57: 21.803 distance: 58 - 59: 25.042 distance: 59 - 60: 48.958 distance: 59 - 62: 39.751 distance: 60 - 61: 27.678 distance: 60 - 66: 34.521 distance: 61 - 97: 58.599 distance: 62 - 63: 41.395 distance: 63 - 64: 13.291 distance: 63 - 65: 13.720 distance: 66 - 67: 24.705 distance: 67 - 68: 53.377 distance: 67 - 70: 17.646 distance: 68 - 69: 57.664 distance: 68 - 74: 12.232 distance: 69 - 105: 57.341 distance: 70 - 71: 52.542 distance: 70 - 72: 65.433 distance: 71 - 73: 5.315 distance: 74 - 75: 57.674 distance: 75 - 76: 38.086 distance: 75 - 78: 43.153 distance: 76 - 77: 50.081 distance: 76 - 85: 40.113 distance: 78 - 79: 62.008 distance: 79 - 80: 43.862 distance: 81 - 82: 8.846 distance: 82 - 83: 49.729 distance: 82 - 84: 35.259 distance: 85 - 86: 47.865 distance: 86 - 89: 55.063 distance: 87 - 88: 17.839 distance: 87 - 97: 44.169 distance: 89 - 90: 4.093 distance: 92 - 94: 14.340 distance: 94 - 95: 13.472 distance: 95 - 96: 39.920 distance: 97 - 98: 41.377 distance: 98 - 99: 59.200 distance: 98 - 101: 17.981 distance: 99 - 100: 36.539 distance: 99 - 105: 50.942 distance: 101 - 102: 55.382 distance: 102 - 103: 64.607 distance: 102 - 104: 63.635 distance: 105 - 106: 38.568 distance: 106 - 107: 39.635 distance: 106 - 109: 53.498 distance: 107 - 108: 30.247 distance: 107 - 113: 50.959 distance: 109 - 110: 6.531 distance: 110 - 111: 38.575 distance: 110 - 112: 4.597 distance: 113 - 114: 40.654 distance: 115 - 116: 56.279 distance: 115 - 117: 56.448 distance: 117 - 118: 55.620 distance: 118 - 119: 39.088 distance: 118 - 121: 57.979 distance: 119 - 120: 24.694 distance: 119 - 129: 27.435 distance: 121 - 122: 38.720 distance: 122 - 123: 39.199 distance: 122 - 124: 20.551 distance: 123 - 125: 19.558 distance: 124 - 126: 37.789 distance: 125 - 127: 19.851 distance: 126 - 127: 35.534 distance: 127 - 128: 33.070 distance: 129 - 130: 16.447 distance: 130 - 131: 18.299 distance: 130 - 133: 7.917 distance: 131 - 132: 16.171 distance: 131 - 136: 28.769 distance: 133 - 134: 7.504 distance: 133 - 135: 54.865