Starting phenix.real_space_refine on Tue Nov 19 11:26:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rtc_4997/11_2024/6rtc_4997.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rtc_4997/11_2024/6rtc_4997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rtc_4997/11_2024/6rtc_4997.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rtc_4997/11_2024/6rtc_4997.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rtc_4997/11_2024/6rtc_4997.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rtc_4997/11_2024/6rtc_4997.cif" } resolution = 3.96 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= 0.004 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 S 68 5.16 5 C 6286 2.51 5 N 1536 2.21 5 O 1680 1.98 5 H 9804 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 19374 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 9687 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 25, 'TRANS': 595} Chain breaks: 2 Restraints were copied for chains: B Time building chain proxies: 26.64, per 1000 atoms: 1.38 Number of scatterers: 19374 At special positions: 0 Unit cell: (97.825, 121.475, 121.475, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 O 1680 8.00 N 1536 7.00 C 6286 6.00 H 9804 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.11 Conformation dependent library (CDL) restraints added in 1.6 seconds 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 7 sheets defined 63.1% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 Processing helix chain 'A' and resid 48 through 56 Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 70 through 95 Proline residue: A 87 - end of helix removed outlier: 4.060A pdb=" N MET A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 118 Proline residue: A 110 - end of helix removed outlier: 4.160A pdb=" N THR A 113 " --> pdb=" O PHE A 109 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 117 " --> pdb=" O THR A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 143 removed outlier: 3.646A pdb=" N SER A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 191 Processing helix chain 'A' and resid 200 through 225 removed outlier: 4.198A pdb=" N LYS A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N TYR A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 247 removed outlier: 4.070A pdb=" N PHE A 239 " --> pdb=" O GLY A 235 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN A 247 " --> pdb=" O ASP A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 276 removed outlier: 3.671A pdb=" N TYR A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 301 Processing helix chain 'A' and resid 329 through 332 Processing helix chain 'A' and resid 333 through 360 removed outlier: 3.549A pdb=" N ALA A 337 " --> pdb=" O MET A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 380 removed outlier: 3.857A pdb=" N ILE A 370 " --> pdb=" O ASN A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 391 through 401 removed outlier: 3.556A pdb=" N GLY A 401 " --> pdb=" O VAL A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 421 removed outlier: 3.671A pdb=" N VAL A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 442 removed outlier: 4.343A pdb=" N LEU A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 449 Processing helix chain 'A' and resid 450 through 457 removed outlier: 4.221A pdb=" N TYR A 454 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 474 removed outlier: 4.284A pdb=" N CYS A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N CYS A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 498 removed outlier: 4.399A pdb=" N ALA A 483 " --> pdb=" O PRO A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 520 removed outlier: 3.729A pdb=" N THR A 519 " --> pdb=" O ASN A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 541 No H-bonds generated for 'chain 'A' and resid 539 through 541' Processing helix chain 'A' and resid 542 through 552 removed outlier: 3.661A pdb=" N ALA A 552 " --> pdb=" O GLN A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 672 No H-bonds generated for 'chain 'A' and resid 670 through 672' Processing helix chain 'A' and resid 676 through 692 Processing helix chain 'A' and resid 703 through 712 removed outlier: 3.657A pdb=" N TYR A 707 " --> pdb=" O HIS A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 740 removed outlier: 3.782A pdb=" N ALA A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN A 740 " --> pdb=" O PHE A 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 24 Processing helix chain 'B' and resid 48 through 56 Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 70 through 95 Proline residue: B 87 - end of helix removed outlier: 4.060A pdb=" N MET B 90 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 118 Proline residue: B 110 - end of helix removed outlier: 4.161A pdb=" N THR B 113 " --> pdb=" O PHE B 109 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 117 " --> pdb=" O THR B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 143 removed outlier: 3.646A pdb=" N SER B 132 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 191 Processing helix chain 'B' and resid 200 through 225 removed outlier: 4.199A pdb=" N LYS B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N TYR B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 247 removed outlier: 4.069A pdb=" N PHE B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN B 247 " --> pdb=" O ASP B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 276 removed outlier: 3.671A pdb=" N TYR B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 301 Processing helix chain 'B' and resid 329 through 332 Processing helix chain 'B' and resid 333 through 360 removed outlier: 3.549A pdb=" N ALA B 337 " --> pdb=" O MET B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 380 removed outlier: 3.857A pdb=" N ILE B 370 " --> pdb=" O ASN B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 383 No H-bonds generated for 'chain 'B' and resid 381 through 383' Processing helix chain 'B' and resid 391 through 401 removed outlier: 3.556A pdb=" N GLY B 401 " --> pdb=" O VAL B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 421 removed outlier: 3.670A pdb=" N VAL B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 442 removed outlier: 4.343A pdb=" N LEU B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 449 Processing helix chain 'B' and resid 450 through 457 removed outlier: 4.221A pdb=" N TYR B 454 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG B 457 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 474 removed outlier: 4.284A pdb=" N CYS B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N CYS B 464 " --> pdb=" O LYS B 460 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 498 removed outlier: 4.399A pdb=" N ALA B 483 " --> pdb=" O PRO B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 520 removed outlier: 3.729A pdb=" N THR B 519 " --> pdb=" O ASN B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 541 No H-bonds generated for 'chain 'B' and resid 539 through 541' Processing helix chain 'B' and resid 542 through 552 removed outlier: 3.661A pdb=" N ALA B 552 " --> pdb=" O GLN B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 672 No H-bonds generated for 'chain 'B' and resid 670 through 672' Processing helix chain 'B' and resid 676 through 692 Processing helix chain 'B' and resid 703 through 712 removed outlier: 3.657A pdb=" N TYR B 707 " --> pdb=" O HIS B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 740 removed outlier: 3.782A pdb=" N ALA B 733 " --> pdb=" O SER B 729 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN B 740 " --> pdb=" O PHE B 736 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 150 removed outlier: 3.582A pdb=" N TYR A 159 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 506 through 507 Processing sheet with id=AA4, first strand: chain 'A' and resid 530 through 533 removed outlier: 6.920A pdb=" N LYS A 530 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ASP A 668 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL A 532 " --> pdb=" O ASP A 668 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A 665 " --> pdb=" O PHE A 698 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL A 700 " --> pdb=" O LEU A 665 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU A 667 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N PHE A 727 " --> pdb=" O ILE A 697 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU A 699 " --> pdb=" O PHE A 727 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 150 removed outlier: 3.582A pdb=" N TYR B 159 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 506 through 507 Processing sheet with id=AA7, first strand: chain 'B' and resid 530 through 533 removed outlier: 6.920A pdb=" N LYS B 530 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ASP B 668 " --> pdb=" O LYS B 530 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL B 532 " --> pdb=" O ASP B 668 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU B 665 " --> pdb=" O PHE B 698 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N VAL B 700 " --> pdb=" O LEU B 665 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU B 667 " --> pdb=" O VAL B 700 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N PHE B 727 " --> pdb=" O ILE B 697 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU B 699 " --> pdb=" O PHE B 727 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 506 hydrogen bonds defined for protein. 1482 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: 6.08 Time building geometry restraints manager: 7.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 9776 1.03 - 1.22: 30 1.22 - 1.42: 4060 1.42 - 1.62: 5624 1.62 - 1.82: 108 Bond restraints: 19598 Sorted by residual: bond pdb=" CG LEU B 340 " pdb=" CD1 LEU B 340 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.57e+00 bond pdb=" CG LEU A 340 " pdb=" CD1 LEU A 340 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.50e+00 bond pdb=" CB PRO A 537 " pdb=" CG PRO A 537 " ideal model delta sigma weight residual 1.492 1.399 0.093 5.00e-02 4.00e+02 3.46e+00 bond pdb=" CB PRO B 537 " pdb=" CG PRO B 537 " ideal model delta sigma weight residual 1.492 1.399 0.093 5.00e-02 4.00e+02 3.46e+00 bond pdb=" CG1 ILE A 387 " pdb=" CD1 ILE A 387 " ideal model delta sigma weight residual 1.513 1.462 0.051 3.90e-02 6.57e+02 1.70e+00 ... (remaining 19593 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 34006 1.94 - 3.88: 1342 3.88 - 5.81: 136 5.81 - 7.75: 12 7.75 - 9.69: 6 Bond angle restraints: 35502 Sorted by residual: angle pdb=" CD1 LEU B 538 " pdb=" CG LEU B 538 " pdb=" CD2 LEU B 538 " ideal model delta sigma weight residual 110.80 104.18 6.62 2.20e+00 2.07e-01 9.06e+00 angle pdb=" CD1 LEU A 538 " pdb=" CG LEU A 538 " pdb=" CD2 LEU A 538 " ideal model delta sigma weight residual 110.80 104.20 6.60 2.20e+00 2.07e-01 8.99e+00 angle pdb=" CA LEU A 538 " pdb=" CB LEU A 538 " pdb=" CG LEU A 538 " ideal model delta sigma weight residual 116.30 125.99 -9.69 3.50e+00 8.16e-02 7.66e+00 angle pdb=" N GLY B 193 " pdb=" CA GLY B 193 " pdb=" C GLY B 193 " ideal model delta sigma weight residual 113.18 119.74 -6.56 2.37e+00 1.78e-01 7.65e+00 angle pdb=" CA LEU B 538 " pdb=" CB LEU B 538 " pdb=" CG LEU B 538 " ideal model delta sigma weight residual 116.30 125.98 -9.68 3.50e+00 8.16e-02 7.65e+00 ... (remaining 35497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.13: 7992 16.13 - 32.25: 916 32.25 - 48.38: 244 48.38 - 64.50: 108 64.50 - 80.63: 10 Dihedral angle restraints: 9270 sinusoidal: 4914 harmonic: 4356 Sorted by residual: dihedral pdb=" CA PHE B 662 " pdb=" C PHE B 662 " pdb=" N HIS B 663 " pdb=" CA HIS B 663 " 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 PHE A 662 " pdb=" C PHE A 662 " pdb=" N HIS A 663 " pdb=" CA HIS A 663 " ideal model delta harmonic sigma weight residual 180.00 157.47 22.53 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA PHE A 108 " pdb=" C PHE A 108 " pdb=" N PHE A 109 " pdb=" CA PHE A 109 " ideal model delta harmonic sigma weight residual -180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 9267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1437 0.089 - 0.178: 121 0.178 - 0.267: 4 0.267 - 0.356: 0 0.356 - 0.445: 2 Chirality restraints: 1564 Sorted by residual: chirality pdb=" CG LEU B 340 " pdb=" CB LEU B 340 " pdb=" CD1 LEU B 340 " pdb=" CD2 LEU B 340 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 4.95e+00 chirality pdb=" CG LEU A 340 " pdb=" CB LEU A 340 " pdb=" CD1 LEU A 340 " pdb=" CD2 LEU A 340 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.91e+00 chirality pdb=" CB ILE B 131 " pdb=" CA ILE B 131 " pdb=" CG1 ILE B 131 " pdb=" CG2 ILE B 131 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1561 not shown) Planarity restraints: 2832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 536 " 0.048 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO B 537 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 537 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 537 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 536 " -0.048 5.00e-02 4.00e+02 7.22e-02 8.34e+00 pdb=" N PRO A 537 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 537 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 537 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 228 " 0.038 5.00e-02 4.00e+02 5.82e-02 5.42e+00 pdb=" N PRO A 229 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 229 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 229 " 0.032 5.00e-02 4.00e+02 ... (remaining 2829 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.29: 3745 2.29 - 2.87: 42627 2.87 - 3.45: 47241 3.45 - 4.02: 62540 4.02 - 4.60: 96516 Nonbonded interactions: 252669 Sorted by model distance: nonbonded pdb=" HH TYR B 345 " pdb=" O SER B 365 " model vdw 1.716 2.450 nonbonded pdb=" HH TYR A 345 " pdb=" O SER A 365 " model vdw 1.716 2.450 nonbonded pdb=" O GLN A 405 " pdb=" HG SER A 408 " model vdw 1.718 2.450 nonbonded pdb=" O GLN B 405 " pdb=" HG SER B 408 " model vdw 1.718 2.450 nonbonded pdb=" HH TYR B 114 " pdb=" OE2 GLU B 368 " model vdw 1.720 2.450 ... (remaining 252664 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=0.50 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: 6.660 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 1.790 Set scattering table: 0.000 Process input model: 57.200 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.0000 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: