Starting phenix.real_space_refine on Sat Aug 3 22:48:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pro_13609/08_2024/7pro_13609.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pro_13609/08_2024/7pro_13609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pro_13609/08_2024/7pro_13609.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pro_13609/08_2024/7pro_13609.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pro_13609/08_2024/7pro_13609.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pro_13609/08_2024/7pro_13609.cif" } resolution = 3.0 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= 0.152 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 24 5.16 5 C 5784 2.51 5 N 1574 2.21 5 O 1650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 112": "OD1" <-> "OD2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A ARG 138": "NH1" <-> "NH2" Residue "A ARG 143": "NH1" <-> "NH2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "A ARG 335": "NH1" <-> "NH2" Residue "A PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 368": "NH1" <-> "NH2" Residue "A PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ASP 416": "OD1" <-> "OD2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A ARG 458": "NH1" <-> "NH2" Residue "A ARG 485": "NH1" <-> "NH2" Residue "A TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 511": "OE1" <-> "OE2" Residue "A ASP 529": "OD1" <-> "OD2" Residue "A ARG 536": "NH1" <-> "NH2" Residue "A ARG 570": "NH1" <-> "NH2" Residue "A ASP 645": "OD1" <-> "OD2" Residue "A GLU 657": "OE1" <-> "OE2" Residue "A ARG 662": "NH1" <-> "NH2" Residue "A ARG 667": "NH1" <-> "NH2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B ARG 115": "NH1" <-> "NH2" Residue "B ARG 138": "NH1" <-> "NH2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B ARG 335": "NH1" <-> "NH2" Residue "B PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 368": "NH1" <-> "NH2" Residue "B PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 403": "OE1" <-> "OE2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B ASP 416": "OD1" <-> "OD2" Residue "B ARG 425": "NH1" <-> "NH2" Residue "B ARG 442": "NH1" <-> "NH2" Residue "B ARG 458": "NH1" <-> "NH2" Residue "B ARG 485": "NH1" <-> "NH2" Residue "B TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 511": "OE1" <-> "OE2" Residue "B ASP 529": "OD1" <-> "OD2" Residue "B ARG 536": "NH1" <-> "NH2" Residue "B ARG 570": "NH1" <-> "NH2" Residue "B ASP 645": "OD1" <-> "OD2" Residue "B GLU 657": "OE1" <-> "OE2" Residue "B ARG 662": "NH1" <-> "NH2" Residue "B ARG 667": "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: 9032 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4516 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 17, 'TRANS': 562} Chain: "B" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4516 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 17, 'TRANS': 562} Time building chain proxies: 5.10, per 1000 atoms: 0.56 Number of scatterers: 9032 At special positions: 0 Unit cell: (117.312, 85.696, 141.44, 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 24 16.00 O 1650 8.00 N 1574 7.00 C 5784 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: 3.50 Conformation dependent library (CDL) restraints added in 1.6 seconds 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2164 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 4 sheets defined 67.3% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 95 through 103 removed outlier: 4.083A pdb=" N GLN A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 144 Proline residue: A 134 - end of helix Processing helix chain 'A' and resid 159 through 205 removed outlier: 3.538A pdb=" N GLN A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 217 through 240 Processing helix chain 'A' and resid 240 through 259 Processing helix chain 'A' and resid 260 through 309 removed outlier: 3.721A pdb=" N ALA A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE A 288 " --> pdb=" O TRP A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 318 through 371 removed outlier: 3.530A pdb=" N SER A 336 " --> pdb=" O ALA A 332 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 392 removed outlier: 3.752A pdb=" N LEU A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 381 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 395 No H-bonds generated for 'chain 'A' and resid 393 through 395' Processing helix chain 'A' and resid 396 through 417 removed outlier: 4.723A pdb=" N TYR A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ARG A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG A 405 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 488 removed outlier: 4.565A pdb=" N ARG A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 516 Processing helix chain 'A' and resid 530 through 537 Processing helix chain 'A' and resid 543 through 554 Processing helix chain 'A' and resid 556 through 563 Processing helix chain 'A' and resid 565 through 569 removed outlier: 4.162A pdb=" N GLN A 568 " --> pdb=" O HIS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 595 Processing helix chain 'A' and resid 609 through 625 Processing helix chain 'A' and resid 660 through 665 Processing helix chain 'A' and resid 670 through 674 removed outlier: 4.186A pdb=" N GLU A 673 " --> pdb=" O VAL A 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 103 Processing helix chain 'B' and resid 109 through 144 Proline residue: B 134 - end of helix Processing helix chain 'B' and resid 159 through 205 removed outlier: 3.539A pdb=" N GLN B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 213 Processing helix chain 'B' and resid 217 through 240 Processing helix chain 'B' and resid 240 through 259 Processing helix chain 'B' and resid 260 through 309 removed outlier: 3.721A pdb=" N ALA B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR B 286 " --> pdb=" O THR B 282 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE B 288 " --> pdb=" O TRP B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 318 through 371 removed outlier: 3.529A pdb=" N SER B 336 " --> pdb=" O ALA B 332 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 392 removed outlier: 3.753A pdb=" N LEU B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL B 381 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 396 through 417 removed outlier: 4.724A pdb=" N TYR B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ARG B 402 " --> pdb=" O GLY B 398 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG B 405 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 488 removed outlier: 4.565A pdb=" N ARG B 485 " --> pdb=" O SER B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 516 Processing helix chain 'B' and resid 530 through 537 Processing helix chain 'B' and resid 543 through 554 Processing helix chain 'B' and resid 556 through 563 Processing helix chain 'B' and resid 565 through 569 removed outlier: 4.161A pdb=" N GLN B 568 " --> pdb=" O HIS B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 595 Processing helix chain 'B' and resid 609 through 625 Processing helix chain 'B' and resid 660 through 665 Processing helix chain 'B' and resid 670 through 674 removed outlier: 4.187A pdb=" N GLU B 673 " --> pdb=" O VAL B 670 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 457 through 464 removed outlier: 4.660A pdb=" N VAL A 446 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N SER A 461 " --> pdb=" O GLU A 444 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLU A 444 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR A 463 " --> pdb=" O ARG A 442 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG A 442 " --> pdb=" O THR A 463 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL A 446 " --> pdb=" O GLN A 495 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLN A 495 " --> pdb=" O VAL A 446 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 517 through 519 removed outlier: 6.566A pdb=" N GLY A 518 " --> pdb=" O PHE A 600 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LYS A 469 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE A 648 " --> pdb=" O LYS A 469 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ALA A 471 " --> pdb=" O ILE A 648 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU A 650 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A 473 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLU A 657 " --> pdb=" O VAL A 649 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 457 through 464 removed outlier: 4.660A pdb=" N VAL B 446 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N SER B 461 " --> pdb=" O GLU B 444 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLU B 444 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR B 463 " --> pdb=" O ARG B 442 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG B 442 " --> pdb=" O THR B 463 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL B 446 " --> pdb=" O GLN B 495 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLN B 495 " --> pdb=" O VAL B 446 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 517 through 519 removed outlier: 6.566A pdb=" N GLY B 518 " --> pdb=" O PHE B 600 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LYS B 469 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE B 648 " --> pdb=" O LYS B 469 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ALA B 471 " --> pdb=" O ILE B 648 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU B 650 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL B 473 " --> pdb=" O LEU B 650 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU B 657 " --> pdb=" O VAL B 649 " (cutoff:3.500A) 600 hydrogen bonds defined for protein. 1782 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: 2.61 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2519 1.33 - 1.45: 1459 1.45 - 1.57: 5174 1.57 - 1.69: 0 1.69 - 1.80: 44 Bond restraints: 9196 Sorted by residual: bond pdb=" CG LEU B 390 " pdb=" CD1 LEU B 390 " ideal model delta sigma weight residual 1.521 1.398 0.123 3.30e-02 9.18e+02 1.39e+01 bond pdb=" CG LEU A 390 " pdb=" CD1 LEU A 390 " ideal model delta sigma weight residual 1.521 1.399 0.122 3.30e-02 9.18e+02 1.38e+01 bond pdb=" C SER B 156 " pdb=" N ALA B 157 " ideal model delta sigma weight residual 1.332 1.296 0.036 1.40e-02 5.10e+03 6.63e+00 bond pdb=" C SER A 156 " pdb=" N ALA A 157 " ideal model delta sigma weight residual 1.332 1.297 0.035 1.40e-02 5.10e+03 6.38e+00 bond pdb=" CB ARG A 170 " pdb=" CG ARG A 170 " ideal model delta sigma weight residual 1.520 1.453 0.067 3.00e-02 1.11e+03 5.04e+00 ... (remaining 9191 not shown) Histogram of bond angle deviations from ideal: 94.75 - 102.65: 38 102.65 - 110.55: 2681 110.55 - 118.45: 4537 118.45 - 126.35: 5112 126.35 - 134.24: 102 Bond angle restraints: 12470 Sorted by residual: angle pdb=" CA TRP A 284 " pdb=" CB TRP A 284 " pdb=" CG TRP A 284 " ideal model delta sigma weight residual 113.60 122.96 -9.36 1.90e+00 2.77e-01 2.43e+01 angle pdb=" CA TRP B 284 " pdb=" CB TRP B 284 " pdb=" CG TRP B 284 " ideal model delta sigma weight residual 113.60 122.95 -9.35 1.90e+00 2.77e-01 2.42e+01 angle pdb=" C LYS B 625 " pdb=" N GLU B 626 " pdb=" CA GLU B 626 " ideal model delta sigma weight residual 122.40 129.10 -6.70 1.45e+00 4.76e-01 2.13e+01 angle pdb=" C LYS A 625 " pdb=" N GLU A 626 " pdb=" CA GLU A 626 " ideal model delta sigma weight residual 122.40 129.10 -6.70 1.45e+00 4.76e-01 2.13e+01 angle pdb=" CA LEU A 586 " pdb=" CB LEU A 586 " pdb=" CG LEU A 586 " ideal model delta sigma weight residual 116.30 132.30 -16.00 3.50e+00 8.16e-02 2.09e+01 ... (remaining 12465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 5041 17.79 - 35.58: 383 35.58 - 53.36: 70 53.36 - 71.15: 10 71.15 - 88.94: 12 Dihedral angle restraints: 5516 sinusoidal: 2156 harmonic: 3360 Sorted by residual: dihedral pdb=" CA MET A 665 " pdb=" C MET A 665 " pdb=" N GLU A 666 " pdb=" CA GLU A 666 " ideal model delta harmonic sigma weight residual 180.00 157.44 22.56 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA MET B 665 " pdb=" C MET B 665 " pdb=" N GLU B 666 " pdb=" CA GLU B 666 " ideal model delta harmonic sigma weight residual 180.00 157.45 22.55 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA SER B 156 " pdb=" C SER B 156 " pdb=" N ALA B 157 " pdb=" CA ALA B 157 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 5513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 887 0.052 - 0.105: 448 0.105 - 0.157: 106 0.157 - 0.209: 20 0.209 - 0.261: 3 Chirality restraints: 1464 Sorted by residual: chirality pdb=" CB VAL A 155 " pdb=" CA VAL A 155 " pdb=" CG1 VAL A 155 " pdb=" CG2 VAL A 155 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB VAL B 155 " pdb=" CA VAL B 155 " pdb=" CG1 VAL B 155 " pdb=" CG2 VAL B 155 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA ASP B 108 " pdb=" N ASP B 108 " pdb=" C ASP B 108 " pdb=" CB ASP B 108 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1461 not shown) Planarity restraints: 1584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 405 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.67e+00 pdb=" C ARG B 405 " -0.045 2.00e-02 2.50e+03 pdb=" O ARG B 405 " 0.017 2.00e-02 2.50e+03 pdb=" N GLN B 406 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 405 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" C ARG A 405 " 0.044 2.00e-02 2.50e+03 pdb=" O ARG A 405 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN A 406 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 138 " 0.091 9.50e-02 1.11e+02 4.60e-02 6.54e+00 pdb=" NE ARG B 138 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG B 138 " -0.042 2.00e-02 2.50e+03 pdb=" NH1 ARG B 138 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG B 138 " 0.017 2.00e-02 2.50e+03 ... (remaining 1581 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1020 2.73 - 3.28: 9288 3.28 - 3.82: 15229 3.82 - 4.36: 18021 4.36 - 4.90: 31384 Nonbonded interactions: 74942 Sorted by model distance: nonbonded pdb=" OH TYR A 537 " pdb=" OE2 GLU B 322 " model vdw 2.192 3.040 nonbonded pdb=" OE2 GLU A 322 " pdb=" OH TYR B 537 " model vdw 2.204 3.040 nonbonded pdb=" O GLY B 566 " pdb=" OG1 THR B 569 " model vdw 2.211 3.040 nonbonded pdb=" O GLY A 566 " pdb=" OG1 THR A 569 " model vdw 2.211 3.040 nonbonded pdb=" O LEU B 586 " pdb=" OG SER B 589 " model vdw 2.342 3.040 ... (remaining 74937 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.290 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 26.880 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.070 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:13.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 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 : 0.012 0.123 9196 Z= 0.771 Angle : 1.092 15.996 12470 Z= 0.610 Chirality : 0.062 0.261 1464 Planarity : 0.009 0.052 1584 Dihedral : 13.800 88.940 3352 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.23), residues: 1156 helix: -0.49 (0.17), residues: 754 sheet: -1.95 (0.58), residues: 58 loop : -2.05 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP A 284 HIS 0.010 0.002 HIS B 132 PHE 0.040 0.004 PHE B 137 TYR 0.044 0.004 TYR B 315 ARG 0.041 0.006 ARG B 138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 516 SER cc_start: 0.7648 (m) cc_final: 0.7418 (m) REVERT: A 568 GLN cc_start: 0.8368 (mm-40) cc_final: 0.8127 (mp10) REVERT: A 585 ARG cc_start: 0.6726 (mtt-85) cc_final: 0.6480 (tpp80) REVERT: A 617 MET cc_start: 0.7925 (tpt) cc_final: 0.7575 (tpp) REVERT: B 400 VAL cc_start: 0.8584 (t) cc_final: 0.8348 (p) REVERT: B 516 SER cc_start: 0.7892 (m) cc_final: 0.7328 (p) REVERT: B 645 ASP cc_start: 0.7077 (t0) cc_final: 0.6851 (t0) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 1.0136 time to fit residues: 130.7703 Evaluate side-chains 93 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- 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: 71.6752 > 50: distance: 78 - 106: 32.365 distance: 83 - 87: 34.858 distance: 84 - 114: 32.104 distance: 87 - 88: 40.814 distance: 88 - 89: 57.861 distance: 88 - 91: 25.630 distance: 89 - 90: 39.308 distance: 89 - 95: 39.849 distance: 90 - 122: 39.123 distance: 91 - 92: 33.592 distance: 92 - 93: 47.955 distance: 92 - 94: 26.639 distance: 95 - 96: 43.496 distance: 96 - 97: 49.150 distance: 96 - 99: 41.457 distance: 97 - 98: 24.472 distance: 97 - 106: 32.551 distance: 99 - 100: 32.783 distance: 100 - 101: 32.203 distance: 101 - 102: 50.604 distance: 102 - 103: 57.375 distance: 103 - 104: 47.653 distance: 103 - 105: 42.027 distance: 106 - 107: 32.865 distance: 107 - 108: 29.448 distance: 107 - 110: 36.184 distance: 108 - 109: 17.637 distance: 108 - 114: 19.585 distance: 110 - 111: 29.361 distance: 111 - 112: 47.442 distance: 111 - 113: 44.087 distance: 114 - 115: 3.376 distance: 115 - 116: 3.055 distance: 116 - 117: 47.392 distance: 116 - 122: 40.497 distance: 118 - 119: 40.372 distance: 119 - 120: 34.162 distance: 119 - 121: 39.613 distance: 122 - 123: 43.067 distance: 123 - 124: 46.268 distance: 123 - 126: 33.143 distance: 124 - 125: 55.411 distance: 124 - 133: 40.174 distance: 126 - 127: 4.316 distance: 127 - 128: 36.625 distance: 127 - 129: 6.599 distance: 128 - 130: 8.168 distance: 129 - 131: 25.125 distance: 130 - 132: 17.917 distance: 131 - 132: 20.682 distance: 133 - 134: 57.732 distance: 134 - 135: 55.421 distance: 134 - 137: 40.918 distance: 135 - 144: 57.201 distance: 138 - 139: 7.881 distance: 139 - 140: 50.694 distance: 140 - 141: 58.169 distance: 141 - 142: 52.421 distance: 141 - 143: 56.735 distance: 144 - 145: 40.914 distance: 145 - 146: 39.805 distance: 145 - 148: 17.455 distance: 146 - 147: 56.042 distance: 146 - 150: 49.116 distance: 148 - 149: 47.491 distance: 150 - 151: 47.273 distance: 151 - 152: 70.689 distance: 151 - 154: 55.609 distance: 152 - 153: 40.433 distance: 152 - 162: 38.383 distance: 154 - 155: 33.736 distance: 155 - 156: 8.829 distance: 155 - 157: 32.695 distance: 156 - 158: 38.447 distance: 157 - 159: 14.146 distance: 158 - 160: 34.077 distance: 159 - 160: 30.708 distance: 160 - 161: 20.327 distance: 162 - 163: 57.235 distance: 163 - 166: 68.992 distance: 164 - 165: 41.195 distance: 164 - 170: 57.275 distance: 166 - 167: 44.227 distance: 167 - 168: 24.461 distance: 167 - 169: 46.941 distance: 170 - 171: 55.502 distance: 170 - 176: 57.074 distance: 171 - 172: 40.603 distance: 171 - 174: 57.872 distance: 172 - 173: 24.495 distance: 172 - 177: 30.090 distance: 174 - 175: 55.528 distance: 175 - 176: 56.363