Starting phenix.real_space_refine on Sat Aug 3 05:44:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1m_36795/08_2024/8k1m_36795.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1m_36795/08_2024/8k1m_36795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1m_36795/08_2024/8k1m_36795.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1m_36795/08_2024/8k1m_36795.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1m_36795/08_2024/8k1m_36795.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1m_36795/08_2024/8k1m_36795.cif" } resolution = 2.9 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= -0.001 sd= 0.064 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 P 3 5.49 5 S 23 5.16 5 C 4573 2.51 5 N 1250 2.21 5 O 1299 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 35": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 93": "OD1" <-> "OD2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "B ARG 206": "NH1" <-> "NH2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "B GLU 386": "OE1" <-> "OE2" Residue "B ARG 391": "NH1" <-> "NH2" Residue "B ARG 473": "NH1" <-> "NH2" Residue "B GLU 505": "OE1" <-> "OE2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C GLU 36": "OE1" <-> "OE2" Residue "C ARG 67": "NH1" <-> "NH2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C ARG 141": "NH1" <-> "NH2" Residue "C ARG 209": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 23": "NH1" <-> "NH2" Residue "D GLU 36": "OE1" <-> "OE2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ASP 90": "OD1" <-> "OD2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "D ARG 141": "NH1" <-> "NH2" Residue "D ARG 209": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7148 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 3847 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 20, 'TRANS': 508} Chain: "C" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1589 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 8, 'TRANS': 202} Chain: "D" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1589 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 8, 'TRANS': 202} Chain: "B" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 123 Unusual residues: {'CDL': 1, 'L9Q': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Time building chain proxies: 5.68, per 1000 atoms: 0.79 Number of scatterers: 7148 At special positions: 0 Unit cell: (67.24, 101.68, 109.06, 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) S 23 16.00 P 3 15.00 O 1299 8.00 N 1250 7.00 C 4573 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 1.7 seconds 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1678 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 0 sheets defined 56.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'D' and resid 48 through 55 Processing helix chain 'D' and resid 78 through 82 removed outlier: 4.351A pdb=" N ARG D 82 " --> pdb=" O VAL D 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 78 through 82' Processing helix chain 'D' and resid 99 through 109 removed outlier: 4.023A pdb=" N ALA D 107 " --> pdb=" O ILE D 103 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG D 108 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 125 removed outlier: 3.621A pdb=" N GLU D 120 " --> pdb=" O ALA D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 150 removed outlier: 3.670A pdb=" N GLN D 142 " --> pdb=" O LYS D 138 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS D 143 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL D 144 " --> pdb=" O ASN D 140 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER D 145 " --> pdb=" O ARG D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 183 removed outlier: 3.909A pdb=" N GLN D 183 " --> pdb=" O GLY D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 201 Processing helix chain 'B' and resid 26 through 36 Processing helix chain 'B' and resid 40 through 63 removed outlier: 3.585A pdb=" N TRP B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 48 " --> pdb=" O TRP B 44 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER B 49 " --> pdb=" O VAL B 45 " (cutoff:3.500A) Proline residue: B 51 - end of helix removed outlier: 4.079A pdb=" N THR B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL B 55 " --> pdb=" O PRO B 51 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ALA B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 79 removed outlier: 3.759A pdb=" N ALA B 72 " --> pdb=" O SER B 68 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 87 removed outlier: 4.237A pdb=" N LEU B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR B 87 " --> pdb=" O GLN B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 101 through 125 removed outlier: 4.940A pdb=" N MET B 105 " --> pdb=" O TRP B 101 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N PHE B 106 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N HIS B 107 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR B 108 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA B 111 " --> pdb=" O HIS B 107 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ALA B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ASP B 125 " --> pdb=" O HIS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 135 removed outlier: 4.820A pdb=" N ASP B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 169 Processing helix chain 'B' and resid 174 through 200 removed outlier: 4.024A pdb=" N VAL B 178 " --> pdb=" O PRO B 174 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE B 191 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN B 200 " --> pdb=" O ALA B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 228 removed outlier: 3.546A pdb=" N GLY B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 236 removed outlier: 4.439A pdb=" N CYS B 236 " --> pdb=" O THR B 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 232 through 236' Processing helix chain 'B' and resid 238 through 244 removed outlier: 3.839A pdb=" N SER B 242 " --> pdb=" O PRO B 238 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 275 removed outlier: 4.286A pdb=" N LEU B 257 " --> pdb=" O TRP B 253 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B 258 " --> pdb=" O TRP B 254 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 306 removed outlier: 3.829A pdb=" N ALA B 304 " --> pdb=" O PRO B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 329 removed outlier: 3.833A pdb=" N SER B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL B 329 " --> pdb=" O VAL B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 336 removed outlier: 7.145A pdb=" N ASP B 335 " --> pdb=" O HIS B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 350 removed outlier: 4.316A pdb=" N THR B 348 " --> pdb=" O ARG B 344 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG B 349 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 388 removed outlier: 3.911A pdb=" N LEU B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE B 368 " --> pdb=" O ALA B 364 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 379 " --> pdb=" O PHE B 375 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N HIS B 384 " --> pdb=" O THR B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 397 Processing helix chain 'B' and resid 405 through 436 removed outlier: 6.935A pdb=" N HIS B 409 " --> pdb=" O TRP B 405 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER B 424 " --> pdb=" O ALA B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 467 removed outlier: 4.142A pdb=" N GLN B 453 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Proline residue: B 455 - end of helix removed outlier: 3.696A pdb=" N LEU B 459 " --> pdb=" O PRO B 455 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LEU B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER B 461 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL B 463 " --> pdb=" O LEU B 459 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 493 Proline residue: B 476 - end of helix removed outlier: 4.903A pdb=" N TRP B 479 " --> pdb=" O THR B 475 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 488 " --> pdb=" O GLY B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 503 removed outlier: 4.087A pdb=" N ASN B 503 " --> pdb=" O GLN B 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 499 through 503' Processing helix chain 'B' and resid 507 through 510 No H-bonds generated for 'chain 'B' and resid 507 through 510' Processing helix chain 'B' and resid 522 through 540 removed outlier: 3.508A pdb=" N ILE B 529 " --> pdb=" O TRP B 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 Processing helix chain 'C' and resid 78 through 82 removed outlier: 4.389A pdb=" N ARG C 82 " --> pdb=" O VAL C 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 78 through 82' Processing helix chain 'C' and resid 99 through 109 Processing helix chain 'C' and resid 115 through 125 removed outlier: 3.621A pdb=" N GLU C 120 " --> pdb=" O ALA C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.671A pdb=" N GLN C 142 " --> pdb=" O LYS C 138 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS C 143 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL C 144 " --> pdb=" O ASN C 140 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER C 145 " --> pdb=" O ARG C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 183 removed outlier: 3.909A pdb=" N GLN C 183 " --> pdb=" O GLY C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 201 286 hydrogen bonds defined for protein. 858 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: 1.70 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1140 1.29 - 1.42: 1755 1.42 - 1.55: 4332 1.55 - 1.68: 6 1.68 - 1.81: 39 Bond restraints: 7272 Sorted by residual: bond pdb=" CB7 CDL B 602 " pdb=" OB8 CDL B 602 " ideal model delta sigma weight residual 1.334 1.404 -0.070 1.10e-02 8.26e+03 4.04e+01 bond pdb=" CA7 CDL B 602 " pdb=" OA8 CDL B 602 " ideal model delta sigma weight residual 1.334 1.399 -0.065 1.10e-02 8.26e+03 3.51e+01 bond pdb=" C ARG C 53 " pdb=" O ARG C 53 " ideal model delta sigma weight residual 1.236 1.162 0.074 1.32e-02 5.74e+03 3.16e+01 bond pdb=" OB2 CDL B 602 " pdb=" PB2 CDL B 602 " ideal model delta sigma weight residual 1.579 1.653 -0.074 1.50e-02 4.44e+03 2.42e+01 bond pdb=" OA2 CDL B 602 " pdb=" PA1 CDL B 602 " ideal model delta sigma weight residual 1.579 1.650 -0.071 1.50e-02 4.44e+03 2.25e+01 ... (remaining 7267 not shown) Histogram of bond angle deviations from ideal: 99.66 - 106.54: 224 106.54 - 113.41: 4103 113.41 - 120.29: 2760 120.29 - 127.17: 2682 127.17 - 134.05: 95 Bond angle restraints: 9864 Sorted by residual: angle pdb=" N ARG D 110 " pdb=" CA ARG D 110 " pdb=" C ARG D 110 " ideal model delta sigma weight residual 112.23 102.32 9.91 1.26e+00 6.30e-01 6.19e+01 angle pdb=" N MET C 109 " pdb=" CA MET C 109 " pdb=" C MET C 109 " ideal model delta sigma weight residual 113.89 101.70 12.19 1.58e+00 4.01e-01 5.95e+01 angle pdb=" C11 CDL B 602 " pdb=" CA5 CDL B 602 " pdb=" OA6 CDL B 602 " ideal model delta sigma weight residual 111.33 119.99 -8.66 1.32e+00 5.72e-01 4.29e+01 angle pdb=" CA GLU B 299 " pdb=" C GLU B 299 " pdb=" N PRO B 300 " ideal model delta sigma weight residual 117.95 122.97 -5.02 7.70e-01 1.69e+00 4.25e+01 angle pdb=" N LEU D 58 " pdb=" CA LEU D 58 " pdb=" C LEU D 58 " ideal model delta sigma weight residual 111.28 118.35 -7.07 1.09e+00 8.42e-01 4.21e+01 ... (remaining 9859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.48: 4053 23.48 - 46.96: 223 46.96 - 70.44: 33 70.44 - 93.92: 5 93.92 - 117.39: 1 Dihedral angle restraints: 4315 sinusoidal: 1674 harmonic: 2641 Sorted by residual: dihedral pdb=" C VAL D 22 " pdb=" N VAL D 22 " pdb=" CA VAL D 22 " pdb=" CB VAL D 22 " ideal model delta harmonic sigma weight residual -122.00 -136.07 14.07 0 2.50e+00 1.60e-01 3.17e+01 dihedral pdb=" C VAL C 22 " pdb=" N VAL C 22 " pdb=" CA VAL C 22 " pdb=" CB VAL C 22 " ideal model delta harmonic sigma weight residual -122.00 -135.78 13.78 0 2.50e+00 1.60e-01 3.04e+01 dihedral pdb=" CA TRP B 458 " pdb=" C TRP B 458 " pdb=" N LEU B 459 " pdb=" CA LEU B 459 " ideal model delta harmonic sigma weight residual 180.00 153.24 26.76 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 4312 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1017 0.076 - 0.153: 132 0.153 - 0.229: 14 0.229 - 0.306: 6 0.306 - 0.382: 4 Chirality restraints: 1173 Sorted by residual: chirality pdb=" CA VAL D 22 " pdb=" N VAL D 22 " pdb=" C VAL D 22 " pdb=" CB VAL D 22 " both_signs ideal model delta sigma weight residual False 2.44 2.06 0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CA VAL C 22 " pdb=" N VAL C 22 " pdb=" C VAL C 22 " pdb=" CB VAL C 22 " both_signs ideal model delta sigma weight residual False 2.44 2.08 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CA ARG D 108 " pdb=" N ARG D 108 " pdb=" C ARG D 108 " pdb=" CB ARG D 108 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 1170 not shown) Planarity restraints: 1239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C38 L9Q B 601 " 0.082 2.00e-02 2.50e+03 8.12e-02 6.60e+01 pdb=" C39 L9Q B 601 " -0.084 2.00e-02 2.50e+03 pdb=" C40 L9Q B 601 " -0.079 2.00e-02 2.50e+03 pdb=" C41 L9Q B 601 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 108 " 0.027 2.00e-02 2.50e+03 5.46e-02 2.98e+01 pdb=" C ARG C 108 " -0.094 2.00e-02 2.50e+03 pdb=" O ARG C 108 " 0.036 2.00e-02 2.50e+03 pdb=" N MET C 109 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 103 " -0.022 2.00e-02 2.50e+03 4.58e-02 2.10e+01 pdb=" C ILE D 103 " 0.079 2.00e-02 2.50e+03 pdb=" O ILE D 103 " -0.029 2.00e-02 2.50e+03 pdb=" N ASP D 104 " -0.027 2.00e-02 2.50e+03 ... (remaining 1236 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2138 2.82 - 3.34: 6495 3.34 - 3.86: 10986 3.86 - 4.38: 13216 4.38 - 4.90: 23314 Nonbonded interactions: 56149 Sorted by model distance: nonbonded pdb=" OH TYR B 33 " pdb=" OD1 ASN B 144 " model vdw 2.303 3.040 nonbonded pdb=" O ALA B 290 " pdb=" OG1 THR C 98 " model vdw 2.310 3.040 nonbonded pdb=" OG SER D 192 " pdb=" OE2 GLU D 197 " model vdw 2.345 3.040 nonbonded pdb=" OG SER C 192 " pdb=" OE2 GLU C 197 " model vdw 2.345 3.040 nonbonded pdb=" O PRO B 472 " pdb=" OG1 THR B 475 " model vdw 2.346 3.040 ... (remaining 56144 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 'C' selection = chain 'D' } 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 individual isotropic 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: 3.920 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.620 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 0.075 7272 Z= 0.468 Angle : 1.083 12.192 9864 Z= 0.659 Chirality : 0.057 0.382 1173 Planarity : 0.007 0.115 1239 Dihedral : 14.615 117.395 2637 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.42 % Allowed : 1.25 % Favored : 98.33 % Cbeta Deviations : 0.36 % 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: -1.85 (0.26), residues: 945 helix: -0.06 (0.24), residues: 501 sheet: -1.37 (0.73), residues: 58 loop : -2.83 (0.26), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 44 HIS 0.005 0.002 HIS D 193 PHE 0.026 0.003 PHE D 19 TYR 0.008 0.001 TYR B 56 ARG 0.014 0.001 ARG B 544 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 287 ARG cc_start: 0.7677 (mtp-110) cc_final: 0.7362 (mtp-110) REVERT: B 296 MET cc_start: 0.8061 (mmt) cc_final: 0.7836 (mmt) REVERT: C 60 LYS cc_start: 0.8993 (tttp) cc_final: 0.8785 (tttp) REVERT: C 215 GLU cc_start: 0.8091 (tp30) cc_final: 0.7005 (mt-10) outliers start: 3 outliers final: 1 residues processed: 112 average time/residue: 1.6729 time to fit residues: 195.0244 Evaluate side-chains 73 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 67 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 0.0270 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 193 HIS D 153 HIS D 193 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7272 Z= 0.196 Angle : 0.599 8.871 9864 Z= 0.302 Chirality : 0.042 0.143 1173 Planarity : 0.004 0.057 1239 Dihedral : 10.782 85.567 1142 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.37 % Allowed : 11.28 % Favored : 86.35 % 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: -1.26 (0.26), residues: 945 helix: 0.55 (0.24), residues: 502 sheet: -1.37 (0.71), residues: 58 loop : -2.73 (0.25), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 44 HIS 0.006 0.001 HIS B 404 PHE 0.014 0.001 PHE B 191 TYR 0.006 0.001 TYR B 432 ARG 0.004 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 76 time to evaluate : 0.850 Fit side-chains REVERT: B 135 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7533 (m-30) REVERT: B 287 ARG cc_start: 0.7629 (mtp-110) cc_final: 0.7406 (mtp-110) REVERT: B 296 MET cc_start: 0.8023 (mmt) cc_final: 0.7753 (mmt) REVERT: B 312 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8294 (mp) REVERT: C 124 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7882 (ptp-170) REVERT: C 215 GLU cc_start: 0.8250 (tp30) cc_final: 0.7265 (mt-10) REVERT: D 67 ARG cc_start: 0.8088 (mtm180) cc_final: 0.7453 (mtp85) REVERT: D 212 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8148 (mttm) outliers start: 17 outliers final: 5 residues processed: 87 average time/residue: 1.5486 time to fit residues: 140.9798 Evaluate side-chains 78 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain D residue 212 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 68 optimal weight: 0.0570 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7272 Z= 0.174 Angle : 0.542 8.522 9864 Z= 0.272 Chirality : 0.041 0.141 1173 Planarity : 0.004 0.038 1239 Dihedral : 9.723 61.079 1138 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.06 % Allowed : 12.67 % Favored : 84.26 % 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: -1.00 (0.27), residues: 945 helix: 0.78 (0.24), residues: 503 sheet: -1.13 (0.72), residues: 58 loop : -2.65 (0.26), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 44 HIS 0.003 0.001 HIS B 404 PHE 0.013 0.001 PHE B 191 TYR 0.005 0.001 TYR B 91 ARG 0.007 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 72 time to evaluate : 0.724 Fit side-chains REVERT: B 93 ASP cc_start: 0.8334 (p0) cc_final: 0.7441 (p0) REVERT: B 135 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7544 (m-30) REVERT: B 272 ARG cc_start: 0.7122 (mmp-170) cc_final: 0.6766 (tpp-160) REVERT: B 287 ARG cc_start: 0.7582 (mtp-110) cc_final: 0.7248 (mtp-110) REVERT: B 296 MET cc_start: 0.8052 (mmt) cc_final: 0.7699 (mmt) REVERT: B 312 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8287 (mp) REVERT: B 350 MET cc_start: 0.8094 (mtt) cc_final: 0.7548 (mtm) REVERT: C 124 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.8036 (ptp-110) REVERT: D 67 ARG cc_start: 0.8044 (mtm180) cc_final: 0.7507 (mtp85) REVERT: D 109 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7935 (mmt) outliers start: 22 outliers final: 5 residues processed: 85 average time/residue: 1.4004 time to fit residues: 124.9201 Evaluate side-chains 74 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain D residue 109 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 9 optimal weight: 0.0020 chunk 40 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 85 optimal weight: 0.0980 chunk 90 optimal weight: 2.9990 chunk 81 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 75 optimal weight: 0.2980 overall best weight: 0.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 GLN D 193 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7272 Z= 0.123 Angle : 0.493 8.545 9864 Z= 0.248 Chirality : 0.040 0.130 1173 Planarity : 0.004 0.029 1239 Dihedral : 9.024 59.989 1138 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.06 % Allowed : 14.21 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.27), residues: 945 helix: 1.04 (0.24), residues: 505 sheet: -0.87 (0.74), residues: 58 loop : -2.55 (0.26), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 44 HIS 0.003 0.001 HIS B 409 PHE 0.011 0.001 PHE B 191 TYR 0.006 0.001 TYR B 91 ARG 0.003 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 70 time to evaluate : 0.788 Fit side-chains REVERT: B 135 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7525 (m-30) REVERT: B 272 ARG cc_start: 0.7118 (mmp-170) cc_final: 0.6733 (tpp-160) REVERT: B 287 ARG cc_start: 0.7565 (mtp-110) cc_final: 0.7246 (mtp-110) REVERT: B 296 MET cc_start: 0.8018 (mmt) cc_final: 0.7704 (mmt) REVERT: B 350 MET cc_start: 0.8158 (mtt) cc_final: 0.7710 (mtm) REVERT: B 491 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.6326 (mm) REVERT: C 13 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.6959 (ptp90) REVERT: D 67 ARG cc_start: 0.8040 (mtm180) cc_final: 0.7527 (mtp85) REVERT: D 212 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8225 (mttm) outliers start: 22 outliers final: 7 residues processed: 82 average time/residue: 1.5037 time to fit residues: 129.3157 Evaluate side-chains 79 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 212 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 77 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 22 optimal weight: 0.0170 chunk 30 optimal weight: 0.0870 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 GLN C 193 HIS D 193 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7272 Z= 0.135 Angle : 0.496 8.197 9864 Z= 0.249 Chirality : 0.040 0.131 1173 Planarity : 0.004 0.047 1239 Dihedral : 8.710 58.638 1138 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.65 % Allowed : 14.35 % Favored : 83.01 % 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: -0.53 (0.27), residues: 945 helix: 1.15 (0.24), residues: 507 sheet: -0.84 (0.74), residues: 58 loop : -2.45 (0.26), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 44 HIS 0.002 0.001 HIS B 404 PHE 0.012 0.001 PHE B 191 TYR 0.007 0.001 TYR B 91 ARG 0.010 0.000 ARG C 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 73 time to evaluate : 0.810 Fit side-chains REVERT: B 67 ARG cc_start: 0.8063 (ttt90) cc_final: 0.7493 (tpt90) REVERT: B 272 ARG cc_start: 0.7139 (mmp-170) cc_final: 0.6741 (tpp-160) REVERT: B 287 ARG cc_start: 0.7588 (mtp-110) cc_final: 0.7336 (mtp-110) REVERT: B 350 MET cc_start: 0.8163 (mtt) cc_final: 0.7789 (mtm) REVERT: B 385 GLN cc_start: 0.8216 (mt0) cc_final: 0.8002 (mt0) REVERT: C 13 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.6981 (ptp90) REVERT: D 67 ARG cc_start: 0.8059 (mtm180) cc_final: 0.7525 (mtp85) REVERT: D 212 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8157 (mttm) outliers start: 19 outliers final: 8 residues processed: 83 average time/residue: 1.4373 time to fit residues: 125.0995 Evaluate side-chains 77 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 212 LYS Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 212 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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: 56.1494 > 50: distance: 133 - 134: 4.103 distance: 134 - 135: 9.791 distance: 134 - 137: 4.105 distance: 135 - 136: 10.893 distance: 135 - 141: 17.435 distance: 137 - 138: 5.620 distance: 138 - 139: 5.949 distance: 138 - 140: 3.102 distance: 141 - 142: 38.345 distance: 142 - 143: 20.281 distance: 143 - 144: 20.101 distance: 143 - 145: 19.110 distance: 144 - 173: 30.719 distance: 145 - 146: 13.557 distance: 146 - 147: 38.551 distance: 146 - 149: 15.884 distance: 147 - 148: 16.403 distance: 147 - 159: 35.136 distance: 149 - 150: 18.374 distance: 150 - 151: 4.727 distance: 150 - 152: 7.495 distance: 151 - 153: 3.516 distance: 153 - 154: 3.778 distance: 157 - 158: 3.299 distance: 159 - 160: 37.577 distance: 160 - 161: 27.798 distance: 160 - 163: 10.446 distance: 161 - 162: 28.957 distance: 161 - 165: 33.298 distance: 163 - 164: 6.825 distance: 165 - 166: 23.703 distance: 166 - 167: 52.843 distance: 166 - 169: 32.833 distance: 167 - 168: 44.930 distance: 167 - 173: 23.379 distance: 169 - 170: 14.445 distance: 170 - 171: 40.541 distance: 170 - 172: 43.281 distance: 173 - 174: 39.151 distance: 174 - 175: 34.821 distance: 174 - 177: 32.931 distance: 175 - 176: 30.058 distance: 175 - 182: 41.494 distance: 177 - 178: 6.982 distance: 178 - 179: 22.322 distance: 179 - 180: 6.272 distance: 179 - 181: 8.067 distance: 182 - 183: 13.813 distance: 183 - 184: 15.226 distance: 183 - 186: 14.349 distance: 184 - 185: 14.311 distance: 184 - 189: 4.053 distance: 186 - 187: 26.263 distance: 186 - 188: 14.607 distance: 189 - 190: 14.937 distance: 190 - 191: 32.400 distance: 190 - 193: 12.524 distance: 191 - 192: 30.415 distance: 191 - 200: 34.558 distance: 193 - 194: 10.567 distance: 194 - 195: 10.481 distance: 195 - 196: 8.903 distance: 196 - 197: 4.480 distance: 200 - 201: 39.520 distance: 200 - 206: 29.830 distance: 201 - 202: 19.232 distance: 201 - 204: 32.084 distance: 202 - 203: 21.901 distance: 202 - 207: 26.587 distance: 204 - 205: 6.931 distance: 205 - 206: 28.326 distance: 207 - 208: 38.326 distance: 208 - 209: 24.516 distance: 208 - 211: 21.891 distance: 209 - 210: 41.672 distance: 209 - 219: 16.333 distance: 211 - 212: 3.873 distance: 212 - 213: 10.447 distance: 212 - 214: 12.147 distance: 213 - 215: 12.797 distance: 214 - 216: 4.390 distance: 215 - 217: 13.186 distance: 217 - 218: 14.462