Starting phenix.real_space_refine on Fri Jan 19 07:56:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r88_24311/01_2024/7r88_24311.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r88_24311/01_2024/7r88_24311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r88_24311/01_2024/7r88_24311.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r88_24311/01_2024/7r88_24311.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r88_24311/01_2024/7r88_24311.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r88_24311/01_2024/7r88_24311.pdb" } resolution = 3.5 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= 0.002 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 66 5.16 5 C 6964 2.51 5 N 1826 2.21 5 O 1931 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ASP 182": "OD1" <-> "OD2" Residue "A ASP 210": "OD1" <-> "OD2" Residue "A ASP 217": "OD1" <-> "OD2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 282": "OD1" <-> "OD2" Residue "A ASP 286": "OD1" <-> "OD2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A ASP 299": "OD1" <-> "OD2" Residue "A ASP 303": "OD1" <-> "OD2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "A TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "A GLU 579": "OE1" <-> "OE2" Residue "A PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 116": "OD1" <-> "OD2" Residue "B ASP 185": "OD1" <-> "OD2" Residue "B ARG 257": "NH1" <-> "NH2" Residue "B ASP 319": "OD1" <-> "OD2" Residue "B ASP 328": "OD1" <-> "OD2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B GLU 351": "OE1" <-> "OE2" Residue "B TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 466": "OD1" <-> "OD2" Residue "B GLU 483": "OE1" <-> "OE2" Residue "B ASP 484": "OD1" <-> "OD2" Residue "B GLU 500": "OE1" <-> "OE2" Residue "B TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C GLU 54": "OE1" <-> "OE2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 94": "OD1" <-> "OD2" Residue "C ARG 108": "NH1" <-> "NH2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "D ASP 61": "OD1" <-> "OD2" Residue "D ASP 75": "OD1" <-> "OD2" Residue "D GLU 99": "OE1" <-> "OE2" Residue "D ASP 102": "OD1" <-> "OD2" Residue "D TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 10787 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4620 Classifications: {'peptide': 587} Link IDs: {'PTRANS': 21, 'TRANS': 565} Chain breaks: 2 Chain: "B" Number of atoms: 4463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4463 Classifications: {'peptide': 562} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 537} Chain breaks: 4 Chain: "C" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 901 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "D" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 803 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 100} Time building chain proxies: 5.81, per 1000 atoms: 0.54 Number of scatterers: 10787 At special positions: 0 Unit cell: (113.288, 108.29, 120.785, 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 66 16.00 O 1931 8.00 N 1826 7.00 C 6964 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 587 " - pdb=" SG CYS A 600 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 117 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 108 " distance=2.03 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: 3.70 Conformation dependent library (CDL) restraints added in 1.8 seconds 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2534 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 8 sheets defined 52.6% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 91 through 101 Processing helix chain 'A' and resid 143 through 156 Processing helix chain 'A' and resid 160 through 175 removed outlier: 4.270A pdb=" N PHE A 164 " --> pdb=" O ASN A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 194 through 208 Processing helix chain 'A' and resid 224 through 241 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 313 through 331 Processing helix chain 'A' and resid 332 through 347 removed outlier: 3.908A pdb=" N HIS A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 381 Processing helix chain 'A' and resid 382 through 402 removed outlier: 5.359A pdb=" N ASN A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 454 Proline residue: A 431 - end of helix Proline residue: A 443 - end of helix removed outlier: 4.213A pdb=" N GLN A 454 " --> pdb=" O ASP A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 491 Proline residue: A 473 - end of helix removed outlier: 4.676A pdb=" N TRP A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 491 " --> pdb=" O TYR A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 524 Proline residue: A 509 - end of helix Processing helix chain 'A' and resid 526 through 545 Processing helix chain 'A' and resid 556 through 564 removed outlier: 3.647A pdb=" N TYR A 564 " --> pdb=" O LYS A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 580 removed outlier: 4.270A pdb=" N TYR A 570 " --> pdb=" O THR A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 613 Processing helix chain 'A' and resid 614 through 617 removed outlier: 4.351A pdb=" N THR A 617 " --> pdb=" O PRO A 614 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 614 through 617' Processing helix chain 'A' and resid 619 through 649 removed outlier: 4.258A pdb=" N ILE A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) Proline residue: A 632 - end of helix removed outlier: 4.430A pdb=" N HIS A 647 " --> pdb=" O LYS A 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 140 through 147 Processing helix chain 'B' and resid 162 through 175 Processing helix chain 'B' and resid 180 through 195 Processing helix chain 'B' and resid 214 through 227 Processing helix chain 'B' and resid 244 through 261 Processing helix chain 'B' and resid 273 through 279 removed outlier: 3.674A pdb=" N LEU B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 307 Processing helix chain 'B' and resid 316 through 325 removed outlier: 4.050A pdb=" N THR B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 353 removed outlier: 3.512A pdb=" N GLU B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS B 352 " --> pdb=" O LEU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 411 Processing helix chain 'B' and resid 413 through 435 Processing helix chain 'B' and resid 444 through 458 Processing helix chain 'B' and resid 458 through 473 removed outlier: 4.488A pdb=" N ASN B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 485 removed outlier: 3.515A pdb=" N GLY B 485 " --> pdb=" O GLU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 517 removed outlier: 4.005A pdb=" N PHE B 493 " --> pdb=" O THR B 489 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE B 494 " --> pdb=" O GLY B 490 " (cutoff:3.500A) Proline residue: B 502 - end of helix Proline residue: B 514 - end of helix removed outlier: 4.352A pdb=" N TRP B 517 " --> pdb=" O MET B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 553 Processing helix chain 'B' and resid 555 through 573 Processing helix chain 'B' and resid 585 through 593 removed outlier: 3.603A pdb=" N TRP B 589 " --> pdb=" O THR B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 608 Processing helix chain 'B' and resid 627 through 632 Processing helix chain 'B' and resid 639 through 665 Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'D' and resid 99 through 103 removed outlier: 3.971A pdb=" N LEU D 103 " --> pdb=" O SER D 100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 77 removed outlier: 6.876A pdb=" N LYS A 70 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N SER A 44 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N VAL A 72 " --> pdb=" O HIS A 42 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA A 43 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU A 110 " --> pdb=" O ALA A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 132 removed outlier: 6.441A pdb=" N ILE A 263 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N CYS A 274 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE A 265 " --> pdb=" O ILE A 272 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 91 through 96 removed outlier: 7.595A pdb=" N PHE B 93 " --> pdb=" O ARG B 50 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ARG B 50 " --> pdb=" O PHE B 93 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL B 95 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N GLU B 48 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.730A pdb=" N GLY B 105 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR B 293 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR B 287 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 26 Processing sheet with id=AA6, first strand: chain 'C' and resid 79 through 81 removed outlier: 5.182A pdb=" N TRP C 66 " --> pdb=" O ARG C 57 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ARG C 57 " --> pdb=" O TRP C 66 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 24 through 27 Processing sheet with id=AA8, first strand: chain 'D' and resid 30 through 32 removed outlier: 6.479A pdb=" N LEU D 31 " --> pdb=" O GLU D 125 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE D 68 " --> pdb=" O TRP D 55 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLN D 57 " --> pdb=" O ARG D 66 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ARG D 66 " --> pdb=" O GLN D 57 " (cutoff:3.500A) 613 hydrogen bonds defined for protein. 1776 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.10 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3433 1.34 - 1.46: 2498 1.46 - 1.58: 4985 1.58 - 1.69: 0 1.69 - 1.81: 105 Bond restraints: 11021 Sorted by residual: bond pdb=" C ILE B 459 " pdb=" N PRO B 460 " ideal model delta sigma weight residual 1.335 1.350 -0.016 1.28e-02 6.10e+03 1.50e+00 bond pdb=" C PHE A 442 " pdb=" N PRO A 443 " ideal model delta sigma weight residual 1.333 1.348 -0.015 1.44e-02 4.82e+03 1.07e+00 bond pdb=" C ASN A 296 " pdb=" N PRO A 297 " ideal model delta sigma weight residual 1.333 1.346 -0.013 1.44e-02 4.82e+03 8.22e-01 bond pdb=" CA VAL B 205 " pdb=" C VAL B 205 " ideal model delta sigma weight residual 1.523 1.534 -0.011 1.27e-02 6.20e+03 7.70e-01 bond pdb=" CA THR B 489 " pdb=" CB THR B 489 " ideal model delta sigma weight residual 1.530 1.544 -0.013 1.69e-02 3.50e+03 6.21e-01 ... (remaining 11016 not shown) Histogram of bond angle deviations from ideal: 100.54 - 107.23: 321 107.23 - 113.92: 6138 113.92 - 120.61: 4609 120.61 - 127.29: 3752 127.29 - 133.98: 98 Bond angle restraints: 14918 Sorted by residual: angle pdb=" C THR B 488 " pdb=" N THR B 489 " pdb=" CA THR B 489 " ideal model delta sigma weight residual 121.54 129.29 -7.75 1.91e+00 2.74e-01 1.65e+01 angle pdb=" N SER B 581 " pdb=" CA SER B 581 " pdb=" C SER B 581 " ideal model delta sigma weight residual 114.56 110.78 3.78 1.27e+00 6.20e-01 8.84e+00 angle pdb=" N VAL A 180 " pdb=" CA VAL A 180 " pdb=" C VAL A 180 " ideal model delta sigma weight residual 111.88 109.23 2.65 1.06e+00 8.90e-01 6.27e+00 angle pdb=" N PHE A 442 " pdb=" CA PHE A 442 " pdb=" C PHE A 442 " ideal model delta sigma weight residual 109.81 115.06 -5.25 2.21e+00 2.05e-01 5.64e+00 angle pdb=" N THR B 489 " pdb=" CA THR B 489 " pdb=" CB THR B 489 " ideal model delta sigma weight residual 110.49 114.26 -3.77 1.69e+00 3.50e-01 4.99e+00 ... (remaining 14913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6060 17.97 - 35.95: 406 35.95 - 53.92: 74 53.92 - 71.90: 8 71.90 - 89.87: 7 Dihedral angle restraints: 6555 sinusoidal: 2605 harmonic: 3950 Sorted by residual: dihedral pdb=" CB CYS A 587 " pdb=" SG CYS A 587 " pdb=" SG CYS A 600 " pdb=" CB CYS A 600 " ideal model delta sinusoidal sigma weight residual -86.00 -46.38 -39.62 1 1.00e+01 1.00e-02 2.21e+01 dihedral pdb=" CA CYS A 600 " pdb=" C CYS A 600 " pdb=" N ALA A 601 " pdb=" CA ALA A 601 " ideal model delta harmonic sigma weight residual 180.00 163.16 16.84 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CB GLU B 189 " pdb=" CG GLU B 189 " pdb=" CD GLU B 189 " pdb=" OE1 GLU B 189 " ideal model delta sinusoidal sigma weight residual 0.00 89.87 -89.87 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 6552 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1301 0.038 - 0.076: 299 0.076 - 0.114: 84 0.114 - 0.152: 11 0.152 - 0.190: 2 Chirality restraints: 1697 Sorted by residual: chirality pdb=" CB VAL B 205 " pdb=" CA VAL B 205 " pdb=" CG1 VAL B 205 " pdb=" CG2 VAL B 205 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.04e-01 chirality pdb=" CA THR B 489 " pdb=" N THR B 489 " pdb=" C THR B 489 " pdb=" CB THR B 489 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.74e-01 chirality pdb=" CA VAL B 210 " pdb=" N VAL B 210 " pdb=" C VAL B 210 " pdb=" CB VAL B 210 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 1694 not shown) Planarity restraints: 1878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 276 " 0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO A 277 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 277 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 277 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 488 " 0.006 2.00e-02 2.50e+03 1.15e-02 1.33e+00 pdb=" C THR B 488 " -0.020 2.00e-02 2.50e+03 pdb=" O THR B 488 " 0.007 2.00e-02 2.50e+03 pdb=" N THR B 489 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 555 " 0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO A 556 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 556 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 556 " 0.015 5.00e-02 4.00e+02 ... (remaining 1875 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2777 2.80 - 3.32: 9800 3.32 - 3.85: 17768 3.85 - 4.37: 19939 4.37 - 4.90: 36069 Nonbonded interactions: 86353 Sorted by model distance: nonbonded pdb=" OH TYR B 54 " pdb=" O GLY B 125 " model vdw 2.274 2.440 nonbonded pdb=" OG SER D 83 " pdb=" OG1 THR D 94 " model vdw 2.288 2.440 nonbonded pdb=" ND2 ASN A 551 " pdb=" OE1 GLU A 554 " model vdw 2.297 2.520 nonbonded pdb=" O ARG B 198 " pdb=" OG SER D 50 " model vdw 2.298 2.440 nonbonded pdb=" OG1 THR C 43 " pdb=" O ASN C 98 " model vdw 2.313 2.440 ... (remaining 86348 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 5.810 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 29.990 Find NCS groups from input model: 0.350 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: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 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 : 0.002 0.037 11021 Z= 0.109 Angle : 0.454 7.753 14918 Z= 0.268 Chirality : 0.036 0.190 1697 Planarity : 0.003 0.033 1878 Dihedral : 12.488 89.872 4012 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.02 % Allowed : 5.76 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: -1.50 (0.21), residues: 1348 helix: 0.30 (0.18), residues: 701 sheet: -1.30 (0.34), residues: 185 loop : -2.89 (0.24), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 229 HIS 0.002 0.000 HIS B 531 PHE 0.006 0.001 PHE C 48 TYR 0.006 0.001 TYR C 115 ARG 0.001 0.000 ARG B 611 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 229 time to evaluate : 1.239 Fit side-chains revert: symmetry clash REVERT: A 121 ARG cc_start: 0.7631 (mtm-85) cc_final: 0.7407 (mtt180) REVERT: A 368 LEU cc_start: 0.8453 (tp) cc_final: 0.8240 (tp) REVERT: A 564 TYR cc_start: 0.8546 (m-80) cc_final: 0.8336 (m-80) REVERT: B 185 ASP cc_start: 0.7818 (m-30) cc_final: 0.7548 (m-30) REVERT: C 81 TYR cc_start: 0.8545 (m-80) cc_final: 0.8331 (m-80) REVERT: C 104 MET cc_start: 0.7995 (mtm) cc_final: 0.7688 (mtm) REVERT: D 99 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8084 (mp0) outliers start: 12 outliers final: 8 residues processed: 240 average time/residue: 0.2474 time to fit residues: 82.3027 Evaluate side-chains 180 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 172 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain C residue 95 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 165 GLN A 206 GLN A 378 ASN A 392 GLN A 462 GLN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS A 510 HIS A 578 ASN A 604 GLN A 607 GLN B 99 GLN B 153 GLN B 199 GLN B 270 HIS B 302 GLN B 409 ASN B 438 HIS B 462 ASN B 526 GLN B 568 ASN B 607 GLN C 75 ASN D 58 GLN D 65 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 11021 Z= 0.406 Angle : 0.666 10.336 14918 Z= 0.334 Chirality : 0.045 0.210 1697 Planarity : 0.004 0.044 1878 Dihedral : 4.539 49.086 1510 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.05 % Allowed : 12.46 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: -0.45 (0.23), residues: 1348 helix: 1.16 (0.19), residues: 702 sheet: -1.29 (0.34), residues: 190 loop : -2.19 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 128 HIS 0.006 0.001 HIS A 510 PHE 0.023 0.002 PHE A 109 TYR 0.019 0.002 TYR B 507 ARG 0.007 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 152 time to evaluate : 1.241 Fit side-chains REVERT: A 324 MET cc_start: 0.8357 (tmm) cc_final: 0.8012 (tmm) REVERT: A 552 ILE cc_start: 0.9272 (mt) cc_final: 0.8974 (pt) REVERT: B 571 TYR cc_start: 0.9161 (t80) cc_final: 0.8920 (t80) outliers start: 36 outliers final: 22 residues processed: 178 average time/residue: 0.2186 time to fit residues: 56.6923 Evaluate side-chains 161 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 139 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 462 ASN Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 117 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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: 56.3594 > 50: distance: 5 - 165: 3.236 distance: 87 - 196: 3.484 distance: 89 - 95: 6.306 distance: 91 - 92: 7.217 distance: 91 - 93: 7.039 distance: 92 - 94: 3.855 distance: 95 - 96: 3.951 distance: 96 - 97: 5.931 distance: 96 - 99: 3.069 distance: 97 - 98: 33.277 distance: 97 - 102: 23.092 distance: 99 - 100: 12.088 distance: 99 - 101: 12.336 distance: 102 - 103: 13.510 distance: 102 - 176: 24.395 distance: 103 - 104: 21.230 distance: 103 - 106: 8.699 distance: 104 - 105: 6.615 distance: 104 - 108: 7.563 distance: 105 - 173: 6.977 distance: 106 - 107: 9.634 distance: 109 - 112: 3.803 distance: 110 - 119: 3.464 distance: 112 - 113: 3.153 distance: 119 - 160: 3.400 distance: 121 - 127: 4.522 distance: 122 - 157: 4.064 distance: 124 - 125: 6.088 distance: 124 - 126: 6.305 distance: 128 - 129: 3.833 distance: 128 - 131: 3.522 distance: 129 - 130: 5.993 distance: 129 - 134: 5.552 distance: 131 - 132: 3.274 distance: 131 - 133: 4.241 distance: 135 - 136: 3.514 distance: 135 - 138: 3.330 distance: 142 - 143: 4.389 distance: 145 - 146: 3.257 distance: 146 - 148: 6.183 distance: 149 - 150: 3.082 distance: 151 - 152: 3.046 distance: 153 - 154: 5.344 distance: 154 - 155: 3.330 distance: 158 - 159: 4.325 distance: 159 - 165: 3.381 distance: 161 - 162: 7.897 distance: 161 - 163: 6.655 distance: 162 - 164: 7.526