Starting phenix.real_space_refine on Thu Jan 16 01:22:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8chb_16659/01_2025/8chb_16659_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8chb_16659/01_2025/8chb_16659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8chb_16659/01_2025/8chb_16659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8chb_16659/01_2025/8chb_16659.map" model { file = "/net/cci-nas-00/data/ceres_data/8chb_16659/01_2025/8chb_16659_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8chb_16659/01_2025/8chb_16659_neut.cif" } resolution = 3.14 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= 0.018 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 36 5.16 5 C 5716 2.51 5 N 1486 2.21 5 O 1678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8916 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4458 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 17, 'TRANS': 561} Chain: "B" Number of atoms: 4458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4458 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 17, 'TRANS': 561} Time building chain proxies: 5.60, per 1000 atoms: 0.63 Number of scatterers: 8916 At special positions: 0 Unit cell: (108.07, 73.83, 138.03, 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 36 16.00 O 1678 8.00 N 1486 7.00 C 5716 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS B 582 " distance=1.94 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.0 seconds 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2132 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 4 sheets defined 63.7% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 removed outlier: 3.527A pdb=" N ALA A 17 " --> pdb=" O LYS A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 44 Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 109 removed outlier: 3.879A pdb=" N LYS A 109 " --> pdb=" O LYS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 120 through 140 removed outlier: 4.356A pdb=" N THR A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N MET A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 162 Processing helix chain 'A' and resid 164 through 210 Proline residue: A 175 - end of helix Proline residue: A 183 - end of helix Processing helix chain 'A' and resid 213 through 219 Processing helix chain 'A' and resid 222 through 274 removed outlier: 3.635A pdb=" N GLY A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 280 through 295 removed outlier: 3.746A pdb=" N GLN A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET A 295 " --> pdb=" O PHE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 322 removed outlier: 3.517A pdb=" N THR A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 388 removed outlier: 3.724A pdb=" N PHE A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 removed outlier: 3.832A pdb=" N HIS A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 436 Processing helix chain 'A' and resid 447 through 454 removed outlier: 4.925A pdb=" N MET A 454 " --> pdb=" O LYS A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 462 Processing helix chain 'A' and resid 481 through 495 Processing helix chain 'A' and resid 514 through 525 removed outlier: 4.066A pdb=" N VAL A 523 " --> pdb=" O GLN A 519 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET A 525 " --> pdb=" O LEU A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 540 Processing helix chain 'A' and resid 560 through 565 Processing helix chain 'A' and resid 569 through 579 removed outlier: 4.118A pdb=" N ALA A 574 " --> pdb=" O TYR A 570 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N GLN A 577 " --> pdb=" O PHE A 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 21 removed outlier: 3.527A pdb=" N ALA B 17 " --> pdb=" O LYS B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 44 Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 64 through 109 removed outlier: 3.880A pdb=" N LYS B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 117 Processing helix chain 'B' and resid 120 through 140 removed outlier: 4.356A pdb=" N THR B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N MET B 132 " --> pdb=" O THR B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 162 Processing helix chain 'B' and resid 164 through 210 Proline residue: B 175 - end of helix Proline residue: B 183 - end of helix Processing helix chain 'B' and resid 213 through 219 Processing helix chain 'B' and resid 222 through 274 removed outlier: 3.635A pdb=" N GLY B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) Proline residue: B 252 - end of helix Processing helix chain 'B' and resid 280 through 295 removed outlier: 3.747A pdb=" N GLN B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET B 295 " --> pdb=" O PHE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 322 removed outlier: 3.518A pdb=" N THR B 302 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE B 304 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR B 305 " --> pdb=" O THR B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 388 removed outlier: 3.724A pdb=" N PHE B 384 " --> pdb=" O LYS B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 436 Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.832A pdb=" N HIS B 416 " --> pdb=" O SER B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 454 removed outlier: 4.925A pdb=" N MET B 454 " --> pdb=" O LYS B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 462 Processing helix chain 'B' and resid 481 through 495 Processing helix chain 'B' and resid 514 through 525 removed outlier: 4.067A pdb=" N VAL B 523 " --> pdb=" O GLN B 519 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET B 525 " --> pdb=" O LEU B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 540 Processing helix chain 'B' and resid 560 through 565 Processing helix chain 'B' and resid 569 through 579 removed outlier: 4.118A pdb=" N ALA B 574 " --> pdb=" O TYR B 570 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N GLN B 577 " --> pdb=" O PHE B 573 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 357 through 364 removed outlier: 6.471A pdb=" N LYS B 358 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N SER B 347 " --> pdb=" O LYS B 358 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N VAL B 360 " --> pdb=" O ARG B 345 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR B 397 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 417 through 421 removed outlier: 6.503A pdb=" N GLY B 418 " --> pdb=" O MET B 501 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ASP B 503 " --> pdb=" O GLY B 418 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B 420 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU B 500 " --> pdb=" O ILE B 531 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ILE B 533 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU B 502 " --> pdb=" O ILE B 533 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 369 " --> pdb=" O GLN B 545 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N LEU B 547 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA B 371 " --> pdb=" O LEU B 547 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N VAL B 549 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N VAL B 373 " --> pdb=" O VAL B 549 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 364 removed outlier: 6.470A pdb=" N LYS A 358 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N SER A 347 " --> pdb=" O LYS A 358 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N VAL A 360 " --> pdb=" O ARG A 345 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR A 397 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 417 through 421 removed outlier: 6.503A pdb=" N GLY A 418 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ASP A 503 " --> pdb=" O GLY A 418 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL A 420 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU A 500 " --> pdb=" O ILE A 531 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ILE A 533 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU A 502 " --> pdb=" O ILE A 533 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A 369 " --> pdb=" O GLN A 545 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N LEU A 547 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA A 371 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N VAL A 549 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N VAL A 373 " --> pdb=" O VAL A 549 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1584 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: 2.42 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1600 1.31 - 1.44: 2077 1.44 - 1.56: 5303 1.56 - 1.69: 0 1.69 - 1.82: 70 Bond restraints: 9050 Sorted by residual: bond pdb=" CZ ARG A 228 " pdb=" NH2 ARG A 228 " ideal model delta sigma weight residual 1.330 1.254 0.076 1.30e-02 5.92e+03 3.44e+01 bond pdb=" CZ ARG B 228 " pdb=" NH2 ARG B 228 " ideal model delta sigma weight residual 1.330 1.254 0.076 1.30e-02 5.92e+03 3.40e+01 bond pdb=" C THR A 555 " pdb=" O THR A 555 " ideal model delta sigma weight residual 1.235 1.187 0.049 9.00e-03 1.23e+04 2.93e+01 bond pdb=" C THR B 555 " pdb=" O THR B 555 " ideal model delta sigma weight residual 1.235 1.187 0.048 9.00e-03 1.23e+04 2.84e+01 bond pdb=" C ASN A 207 " pdb=" O ASN A 207 " ideal model delta sigma weight residual 1.236 1.188 0.049 1.15e-02 7.56e+03 1.80e+01 ... (remaining 9045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 10262 2.39 - 4.78: 1808 4.78 - 7.18: 170 7.18 - 9.57: 4 9.57 - 11.96: 2 Bond angle restraints: 12246 Sorted by residual: angle pdb=" N PHE A 304 " pdb=" CA PHE A 304 " pdb=" C PHE A 304 " ideal model delta sigma weight residual 111.36 117.90 -6.54 1.09e+00 8.42e-01 3.60e+01 angle pdb=" N PHE B 304 " pdb=" CA PHE B 304 " pdb=" C PHE B 304 " ideal model delta sigma weight residual 111.36 117.89 -6.53 1.09e+00 8.42e-01 3.59e+01 angle pdb=" N ASN B 207 " pdb=" CA ASN B 207 " pdb=" C ASN B 207 " ideal model delta sigma weight residual 110.97 104.55 6.42 1.09e+00 8.42e-01 3.47e+01 angle pdb=" N ASN A 207 " pdb=" CA ASN A 207 " pdb=" C ASN A 207 " ideal model delta sigma weight residual 110.97 104.59 6.38 1.09e+00 8.42e-01 3.43e+01 angle pdb=" N ARG A 571 " pdb=" CA ARG A 571 " pdb=" C ARG A 571 " ideal model delta sigma weight residual 111.69 104.99 6.70 1.23e+00 6.61e-01 2.97e+01 ... (remaining 12241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 4905 17.03 - 34.07: 430 34.07 - 51.10: 98 51.10 - 68.13: 36 68.13 - 85.16: 18 Dihedral angle restraints: 5487 sinusoidal: 2169 harmonic: 3318 Sorted by residual: dihedral pdb=" CA ILE A 364 " pdb=" C ILE A 364 " pdb=" N GLU A 365 " pdb=" CA GLU A 365 " ideal model delta harmonic sigma weight residual -180.00 -152.17 -27.83 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA ILE B 364 " pdb=" C ILE B 364 " pdb=" N GLU B 365 " pdb=" CA GLU B 365 " ideal model delta harmonic sigma weight residual 180.00 -152.20 -27.80 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA GLN A 342 " pdb=" C GLN A 342 " pdb=" N LEU A 343 " pdb=" CA LEU A 343 " ideal model delta harmonic sigma weight residual 180.00 152.87 27.13 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 5484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 952 0.069 - 0.138: 358 0.138 - 0.207: 120 0.207 - 0.276: 42 0.276 - 0.346: 8 Chirality restraints: 1480 Sorted by residual: chirality pdb=" CA SER B 507 " pdb=" N SER B 507 " pdb=" C SER B 507 " pdb=" CB SER B 507 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA SER A 507 " pdb=" N SER A 507 " pdb=" C SER A 507 " pdb=" CB SER A 507 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CB THR B 555 " pdb=" CA THR B 555 " pdb=" OG1 THR B 555 " pdb=" CG2 THR B 555 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 1477 not shown) Planarity restraints: 1540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 268 " -0.087 2.00e-02 2.50e+03 4.82e-02 4.64e+01 pdb=" CG TYR B 268 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR B 268 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR B 268 " 0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR B 268 " 0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR B 268 " 0.022 2.00e-02 2.50e+03 pdb=" CZ TYR B 268 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 268 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 268 " 0.087 2.00e-02 2.50e+03 4.80e-02 4.61e+01 pdb=" CG TYR A 268 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 268 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR A 268 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR A 268 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR A 268 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR A 268 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 268 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 413 " 0.060 2.00e-02 2.50e+03 3.55e-02 3.14e+01 pdb=" CG TRP B 413 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TRP B 413 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP B 413 " -0.027 2.00e-02 2.50e+03 pdb=" NE1 TRP B 413 " -0.039 2.00e-02 2.50e+03 pdb=" CE2 TRP B 413 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP B 413 " -0.052 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 413 " 0.040 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 413 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP B 413 " 0.045 2.00e-02 2.50e+03 ... (remaining 1537 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 4447 2.99 - 3.47: 9701 3.47 - 3.94: 13930 3.94 - 4.42: 15782 4.42 - 4.90: 25564 Nonbonded interactions: 69424 Sorted by model distance: nonbonded pdb=" OH TYR A 437 " pdb=" OE2 GLU B 225 " model vdw 2.512 3.040 nonbonded pdb=" OG SER A 428 " pdb=" NE2 GLN B 208 " model vdw 2.521 3.120 nonbonded pdb=" O VAL B 182 " pdb=" CA PRO B 183 " model vdw 2.533 2.776 nonbonded pdb=" O VAL A 182 " pdb=" CA PRO A 183 " model vdw 2.533 2.776 nonbonded pdb=" O GLY B 298 " pdb=" OG1 THR B 301 " model vdw 2.537 3.040 ... (remaining 69419 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: 0.04 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: 2.920 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: 23.290 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 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 0.105 9050 Z= 0.799 Angle : 1.748 11.960 12246 Z= 1.185 Chirality : 0.088 0.346 1480 Planarity : 0.013 0.157 1540 Dihedral : 15.261 85.163 3352 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.64 % Allowed : 8.18 % Favored : 90.18 % Cbeta Deviations : 0.19 % 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: -1.52 (0.22), residues: 1154 helix: -0.72 (0.17), residues: 748 sheet: 0.40 (0.74), residues: 54 loop : -1.55 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.014 TRP B 413 HIS 0.012 0.003 HIS B 416 PHE 0.055 0.006 PHE A 286 TYR 0.087 0.012 TYR B 268 ARG 0.040 0.002 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8541 (mm) REVERT: A 358 LYS cc_start: 0.7389 (ttpt) cc_final: 0.7066 (mtmm) REVERT: A 390 PHE cc_start: 0.7410 (t80) cc_final: 0.6989 (t80) REVERT: A 391 TYR cc_start: 0.7864 (m-80) cc_final: 0.7606 (m-10) REVERT: A 427 MET cc_start: 0.8154 (mmt) cc_final: 0.7682 (mmt) REVERT: B 358 LYS cc_start: 0.7436 (ttpt) cc_final: 0.7140 (mtmm) REVERT: B 390 PHE cc_start: 0.7384 (t80) cc_final: 0.7046 (t80) REVERT: B 391 TYR cc_start: 0.7907 (m-10) cc_final: 0.7648 (m-10) REVERT: B 427 MET cc_start: 0.8100 (mmt) cc_final: 0.7724 (mmt) outliers start: 16 outliers final: 6 residues processed: 143 average time/residue: 0.2434 time to fit residues: 46.4759 Evaluate side-chains 87 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 571 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 58 optimal weight: 0.0470 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 0.0870 chunk 54 optimal weight: 0.9990 chunk 66 optimal weight: 0.1980 chunk 103 optimal weight: 6.9990 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 292 GLN B 208 GLN B 292 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.166823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.131388 restraints weight = 13289.317| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.36 r_work: 0.3645 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9050 Z= 0.200 Angle : 0.667 6.179 12246 Z= 0.352 Chirality : 0.043 0.184 1480 Planarity : 0.004 0.043 1540 Dihedral : 5.777 43.163 1256 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.02 % Allowed : 11.66 % Favored : 87.32 % 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: 0.91 (0.24), residues: 1154 helix: 1.40 (0.19), residues: 740 sheet: 0.93 (0.71), residues: 54 loop : -1.09 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 164 HIS 0.005 0.001 HIS A 141 PHE 0.015 0.001 PHE A 390 TYR 0.010 0.001 TYR B 456 ARG 0.004 0.001 ARG B 228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 MET cc_start: 0.7953 (tmm) cc_final: 0.7576 (tmm) REVERT: A 529 THR cc_start: 0.7449 (m) cc_final: 0.6658 (p) REVERT: B 188 MET cc_start: 0.7978 (tmm) cc_final: 0.7593 (tmm) REVERT: B 427 MET cc_start: 0.8094 (mmt) cc_final: 0.7828 (mmt) outliers start: 10 outliers final: 8 residues processed: 103 average time/residue: 0.1953 time to fit residues: 29.6694 Evaluate side-chains 82 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 532 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.7716 > 50: distance: 66 - 85: 8.157 distance: 70 - 94: 14.198 distance: 76 - 102: 18.106 distance: 80 - 85: 9.943 distance: 81 - 110: 21.624 distance: 85 - 86: 18.199 distance: 86 - 87: 14.136 distance: 86 - 89: 15.242 distance: 87 - 88: 16.753 distance: 87 - 94: 12.424 distance: 89 - 90: 9.952 distance: 90 - 91: 4.467 distance: 91 - 92: 3.310 distance: 94 - 95: 8.567 distance: 95 - 96: 13.892 distance: 95 - 98: 17.435 distance: 96 - 97: 6.860 distance: 96 - 102: 9.927 distance: 98 - 99: 15.404 distance: 98 - 100: 12.371 distance: 99 - 101: 17.258 distance: 102 - 103: 13.337 distance: 103 - 104: 19.940 distance: 103 - 106: 10.744 distance: 104 - 105: 40.695 distance: 104 - 110: 6.055 distance: 106 - 107: 9.529 distance: 107 - 108: 7.156 distance: 107 - 109: 8.122 distance: 110 - 111: 15.018 distance: 111 - 112: 21.304 distance: 111 - 114: 40.598 distance: 112 - 113: 14.911 distance: 112 - 115: 5.193 distance: 115 - 116: 5.134 distance: 116 - 117: 7.255 distance: 116 - 119: 14.251 distance: 117 - 118: 36.123 distance: 117 - 124: 9.942 distance: 119 - 120: 13.273 distance: 120 - 121: 3.293 distance: 124 - 125: 10.327 distance: 125 - 128: 5.000 distance: 126 - 127: 26.893 distance: 126 - 133: 21.769 distance: 128 - 129: 4.835 distance: 129 - 130: 4.762 distance: 130 - 131: 4.829 distance: 130 - 132: 4.011 distance: 133 - 134: 18.063 distance: 134 - 135: 7.942 distance: 134 - 137: 5.493 distance: 135 - 136: 8.788 distance: 135 - 142: 6.134 distance: 137 - 138: 3.947 distance: 138 - 139: 3.377 distance: 139 - 140: 3.787 distance: 142 - 143: 3.464 distance: 143 - 144: 9.740 distance: 143 - 146: 6.938 distance: 144 - 145: 23.810 distance: 144 - 151: 10.534 distance: 146 - 147: 10.505 distance: 147 - 148: 4.087 distance: 151 - 152: 7.444 distance: 152 - 153: 4.223 distance: 152 - 155: 3.189 distance: 153 - 154: 6.781 distance: 153 - 159: 5.467 distance: 155 - 156: 4.304 distance: 156 - 158: 3.068 distance: 159 - 160: 6.571 distance: 160 - 163: 10.066 distance: 161 - 162: 21.446 distance: 161 - 166: 8.913 distance: 163 - 164: 3.754 distance: 163 - 165: 7.196