Starting phenix.real_space_refine on Thu May 15 08:53:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qh0_53151/05_2025/9qh0_53151.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qh0_53151/05_2025/9qh0_53151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qh0_53151/05_2025/9qh0_53151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qh0_53151/05_2025/9qh0_53151.map" model { file = "/net/cci-nas-00/data/ceres_data/9qh0_53151/05_2025/9qh0_53151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qh0_53151/05_2025/9qh0_53151.cif" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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 64 5.16 5 C 8099 2.51 5 N 2278 2.21 5 O 2505 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12946 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4180 Classifications: {'peptide': 549} Link IDs: {'PTRANS': 25, 'TRANS': 523} Chain: "B" Number of atoms: 4180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4180 Classifications: {'peptide': 549} Link IDs: {'PTRANS': 25, 'TRANS': 523} Chain: "C" Number of atoms: 4168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4168 Classifications: {'peptide': 549} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 25, 'TRANS': 523} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 411 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 8, 'TRANS': 46} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 7.70, per 1000 atoms: 0.59 Number of scatterers: 12946 At special positions: 0 Unit cell: (90.52, 113.15, 108.04, 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 64 16.00 O 2505 8.00 N 2278 7.00 C 8099 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 - 3.00 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: 2.90 Conformation dependent library (CDL) restraints added in 1.6 seconds 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3114 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 13 sheets defined 38.4% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 85 through 100 Proline residue: A 98 - end of helix Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 125 through 141 removed outlier: 4.408A pdb=" N VAL A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 171 Processing helix chain 'A' and resid 197 through 212 removed outlier: 3.575A pdb=" N ALA A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL A 205 " --> pdb=" O MET A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 227 Processing helix chain 'A' and resid 239 through 258 removed outlier: 5.900A pdb=" N ALA A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ARG A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 285 Processing helix chain 'A' and resid 289 through 312 Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 397 through 413 removed outlier: 4.266A pdb=" N ALA A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 454 removed outlier: 3.580A pdb=" N ALA A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 489 Processing helix chain 'A' and resid 515 through 539 Processing helix chain 'B' and resid 67 through 71 Processing helix chain 'B' and resid 85 through 100 Proline residue: B 98 - end of helix Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 125 through 141 removed outlier: 4.439A pdb=" N VAL B 129 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 227 removed outlier: 3.587A pdb=" N ALA B 204 " --> pdb=" O GLN B 200 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN B 213 " --> pdb=" O HIS B 209 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL B 214 " --> pdb=" O GLU B 210 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL B 215 " --> pdb=" O GLN B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 258 removed outlier: 5.871A pdb=" N ALA B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ARG B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 285 removed outlier: 3.562A pdb=" N ARG B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 311 Processing helix chain 'B' and resid 358 through 362 removed outlier: 3.526A pdb=" N ALA B 362 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 397 through 412 Processing helix chain 'B' and resid 437 through 454 removed outlier: 3.552A pdb=" N VAL B 443 " --> pdb=" O SER B 439 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS B 444 " --> pdb=" O MET B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 541 removed outlier: 3.510A pdb=" N MET B 519 " --> pdb=" O THR B 515 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA B 540 " --> pdb=" O VAL B 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 70 Processing helix chain 'C' and resid 85 through 100 Proline residue: C 98 - end of helix Processing helix chain 'C' and resid 125 through 142 removed outlier: 4.220A pdb=" N VAL C 129 " --> pdb=" O ASN C 125 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 172 Processing helix chain 'C' and resid 197 through 212 removed outlier: 3.768A pdb=" N ALA C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 205 " --> pdb=" O MET C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 227 Processing helix chain 'C' and resid 239 through 258 removed outlier: 5.985A pdb=" N ALA C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ARG C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 285 Processing helix chain 'C' and resid 289 through 311 Processing helix chain 'C' and resid 358 through 362 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.573A pdb=" N VAL C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 412 removed outlier: 3.611A pdb=" N GLY C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 415 No H-bonds generated for 'chain 'C' and resid 413 through 415' Processing helix chain 'C' and resid 437 through 453 Processing helix chain 'C' and resid 515 through 541 removed outlier: 3.734A pdb=" N GLN C 539 " --> pdb=" O GLY C 535 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA C 540 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C 541 " --> pdb=" O MET C 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 1042 through 1046 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 11 removed outlier: 6.327A pdb=" N ALA A 39 " --> pdb=" O VAL A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 163 removed outlier: 3.614A pdb=" N GLY A 181 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR A 156 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU A 175 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 10.321A pdb=" N GLU A 190 " --> pdb=" O ASP A 508 " (cutoff:3.500A) removed outlier: 10.159A pdb=" N ASP A 508 " --> pdb=" O GLU A 190 " (cutoff:3.500A) removed outlier: 10.207A pdb=" N GLU A 192 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 9.738A pdb=" N GLN A 506 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N GLN A 194 " --> pdb=" O ALA A 504 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N ALA A 504 " --> pdb=" O GLN A 194 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 376 through 381 removed outlier: 6.212A pdb=" N LEU A 377 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N SER A 429 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N HIS A 379 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE A 431 " --> pdb=" O HIS A 379 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ASN A 381 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N GLU A 433 " --> pdb=" O ASN A 381 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLN A 349 " --> pdb=" O THR A 432 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 363 through 366 Processing sheet with id=AA5, first strand: chain 'B' and resid 5 through 11 removed outlier: 6.198A pdb=" N ALA B 39 " --> pdb=" O VAL B 118 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 160 through 163 removed outlier: 4.152A pdb=" N TYR B 156 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU B 175 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 10.486A pdb=" N GLU B 190 " --> pdb=" O ASP B 508 " (cutoff:3.500A) removed outlier: 10.326A pdb=" N ASP B 508 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 10.130A pdb=" N GLU B 192 " --> pdb=" O GLN B 506 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N GLN B 506 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N GLN B 194 " --> pdb=" O ALA B 504 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N ALA B 504 " --> pdb=" O GLN B 194 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 323 through 324 removed outlier: 3.612A pdb=" N THR D1011 " --> pdb=" O ILE B 324 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 376 through 381 removed outlier: 6.402A pdb=" N LEU B 377 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N SER B 429 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N HIS B 379 " --> pdb=" O SER B 429 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE B 431 " --> pdb=" O HIS B 379 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ASN B 381 " --> pdb=" O ILE B 431 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLU B 433 " --> pdb=" O ASN B 381 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N GLN B 349 " --> pdb=" O THR B 432 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 363 through 367 Processing sheet with id=AB1, first strand: chain 'C' and resid 5 through 11 removed outlier: 6.143A pdb=" N ALA C 39 " --> pdb=" O VAL C 118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 160 through 163 removed outlier: 4.085A pdb=" N TYR C 156 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU C 175 " --> pdb=" O TYR C 156 " (cutoff:3.500A) removed outlier: 10.429A pdb=" N GLU C 190 " --> pdb=" O ASP C 508 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N ASP C 508 " --> pdb=" O GLU C 190 " (cutoff:3.500A) removed outlier: 10.171A pdb=" N GLU C 192 " --> pdb=" O GLN C 506 " (cutoff:3.500A) removed outlier: 9.746A pdb=" N GLN C 506 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 9.213A pdb=" N GLN C 194 " --> pdb=" O ALA C 504 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N ALA C 504 " --> pdb=" O GLN C 194 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA C 504 " --> pdb=" O ALA C 496 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 327 through 331 removed outlier: 6.156A pdb=" N GLN C 349 " --> pdb=" O THR C 432 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU C 377 " --> pdb=" O VAL C 427 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N SER C 429 " --> pdb=" O LEU C 377 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N HIS C 379 " --> pdb=" O SER C 429 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE C 431 " --> pdb=" O HIS C 379 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ASN C 381 " --> pdb=" O ILE C 431 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N GLU C 433 " --> pdb=" O ASN C 381 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 363 through 366 748 hydrogen bonds defined for protein. 2037 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: 3.99 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4446 1.34 - 1.45: 1410 1.45 - 1.57: 7164 1.57 - 1.69: 0 1.69 - 1.81: 125 Bond restraints: 13145 Sorted by residual: bond pdb=" CB VAL B 179 " pdb=" CG2 VAL B 179 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.36e+00 bond pdb=" CG MET A 466 " pdb=" SD MET A 466 " ideal model delta sigma weight residual 1.803 1.767 0.036 2.50e-02 1.60e+03 2.07e+00 bond pdb=" CG LEU A 310 " pdb=" CD1 LEU A 310 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.84e+00 bond pdb=" CB PRO A 314 " pdb=" CG PRO A 314 " ideal model delta sigma weight residual 1.492 1.559 -0.067 5.00e-02 4.00e+02 1.79e+00 bond pdb=" CG MET B 466 " pdb=" SD MET B 466 " ideal model delta sigma weight residual 1.803 1.771 0.032 2.50e-02 1.60e+03 1.60e+00 ... (remaining 13140 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 17380 2.03 - 4.06: 390 4.06 - 6.09: 43 6.09 - 8.12: 3 8.12 - 10.15: 1 Bond angle restraints: 17817 Sorted by residual: angle pdb=" CA LEU B 177 " pdb=" CB LEU B 177 " pdb=" CG LEU B 177 " ideal model delta sigma weight residual 116.30 126.45 -10.15 3.50e+00 8.16e-02 8.41e+00 angle pdb=" CA GLN B 520 " pdb=" CB GLN B 520 " pdb=" CG GLN B 520 " ideal model delta sigma weight residual 114.10 119.83 -5.73 2.00e+00 2.50e-01 8.22e+00 angle pdb=" N ASN C 524 " pdb=" CA ASN C 524 " pdb=" C ASN C 524 " ideal model delta sigma weight residual 111.69 108.25 3.44 1.23e+00 6.61e-01 7.83e+00 angle pdb=" CA MET A 466 " pdb=" CB MET A 466 " pdb=" CG MET A 466 " ideal model delta sigma weight residual 114.10 119.56 -5.46 2.00e+00 2.50e-01 7.45e+00 angle pdb=" N GLY B 150 " pdb=" CA GLY B 150 " pdb=" C GLY B 150 " ideal model delta sigma weight residual 112.10 107.24 4.86 1.82e+00 3.02e-01 7.14e+00 ... (remaining 17812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 7217 16.69 - 33.37: 626 33.37 - 50.06: 148 50.06 - 66.74: 25 66.74 - 83.43: 21 Dihedral angle restraints: 8037 sinusoidal: 3191 harmonic: 4846 Sorted by residual: dihedral pdb=" CD ARG A 83 " pdb=" NE ARG A 83 " pdb=" CZ ARG A 83 " pdb=" NH1 ARG A 83 " ideal model delta sinusoidal sigma weight residual 0.00 -81.48 81.48 1 1.00e+01 1.00e-02 8.18e+01 dihedral pdb=" CD ARG C 259 " pdb=" NE ARG C 259 " pdb=" CZ ARG C 259 " pdb=" NH1 ARG C 259 " ideal model delta sinusoidal sigma weight residual 0.00 -68.28 68.28 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CD ARG B 545 " pdb=" NE ARG B 545 " pdb=" CZ ARG B 545 " pdb=" NH1 ARG B 545 " ideal model delta sinusoidal sigma weight residual 0.00 -68.24 68.24 1 1.00e+01 1.00e-02 6.04e+01 ... (remaining 8034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1418 0.045 - 0.089: 473 0.089 - 0.133: 143 0.133 - 0.178: 14 0.178 - 0.222: 4 Chirality restraints: 2052 Sorted by residual: chirality pdb=" CA MET A 466 " pdb=" N MET A 466 " pdb=" C MET A 466 " pdb=" CB MET A 466 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA TYR B 258 " pdb=" N TYR B 258 " pdb=" C TYR B 258 " pdb=" CB TYR B 258 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ILE B 548 " pdb=" N ILE B 548 " pdb=" C ILE B 548 " pdb=" CB ILE B 548 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.42e-01 ... (remaining 2049 not shown) Planarity restraints: 2366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 83 " 0.943 9.50e-02 1.11e+02 4.24e-01 1.18e+02 pdb=" NE ARG A 83 " -0.077 2.00e-02 2.50e+03 pdb=" CZ ARG A 83 " 0.043 2.00e-02 2.50e+03 pdb=" NH1 ARG A 83 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 83 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 259 " 0.861 9.50e-02 1.11e+02 3.87e-01 1.02e+02 pdb=" NE ARG C 259 " -0.073 2.00e-02 2.50e+03 pdb=" CZ ARG C 259 " 0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG C 259 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG C 259 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 545 " 0.849 9.50e-02 1.11e+02 3.82e-01 1.01e+02 pdb=" NE ARG B 545 " -0.073 2.00e-02 2.50e+03 pdb=" CZ ARG B 545 " 0.052 2.00e-02 2.50e+03 pdb=" NH1 ARG B 545 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG B 545 " 0.001 2.00e-02 2.50e+03 ... (remaining 2363 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1153 2.74 - 3.28: 12193 3.28 - 3.82: 21362 3.82 - 4.36: 25944 4.36 - 4.90: 45356 Nonbonded interactions: 106008 Sorted by model distance: nonbonded pdb=" OE2 GLU A 430 " pdb=" OH TYR B 68 " model vdw 2.199 3.040 nonbonded pdb=" O ILE A 260 " pdb=" NH1 ARG A 266 " model vdw 2.231 3.120 nonbonded pdb=" OH TYR C 258 " pdb=" OE2 GLU C 301 " model vdw 2.232 3.040 nonbonded pdb=" OH TYR A 156 " pdb=" OD1 ASP A 159 " model vdw 2.267 3.040 nonbonded pdb=" O VAL B 179 " pdb=" NE2 GLN B 212 " model vdw 2.289 3.120 ... (remaining 106003 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' and (resid 1 through 397 or (resid 398 through 399 and (name N or nam \ e CA or name C or name O or name CB )) or resid 400 through 549)) selection = (chain 'B' and (resid 1 through 397 or (resid 398 through 399 and (name N or nam \ e CA or name C or name O or name CB )) or resid 400 through 549)) selection = chain 'C' } 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: 2.970 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 29.430 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 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:11.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 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 : 0.005 0.067 13145 Z= 0.201 Angle : 0.700 10.153 17817 Z= 0.384 Chirality : 0.048 0.222 2052 Planarity : 0.022 0.424 2366 Dihedral : 14.003 83.431 4923 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: 0.54 (0.20), residues: 1694 helix: 0.96 (0.22), residues: 561 sheet: 1.25 (0.25), residues: 399 loop : -0.58 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 231 HIS 0.007 0.001 HIS B 379 PHE 0.043 0.002 PHE C 493 TYR 0.041 0.002 TYR C 11 ARG 0.061 0.005 ARG B 545 Details of bonding type rmsd hydrogen bonds : bond 0.12801 ( 748) hydrogen bonds : angle 5.33940 ( 2037) covalent geometry : bond 0.00464 (13145) covalent geometry : angle 0.70018 (17817) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 1.517 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6695 (pmm) cc_final: 0.6294 (mtt) REVERT: A 19 GLU cc_start: 0.8342 (tt0) cc_final: 0.7884 (tm-30) REVERT: A 389 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7901 (mm-30) REVERT: A 405 ARG cc_start: 0.8148 (tpt-90) cc_final: 0.7708 (tpp80) REVERT: A 512 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7963 (mt-10) REVERT: B 83 ARG cc_start: 0.7371 (ptt180) cc_final: 0.6932 (ppt-90) REVERT: B 201 MET cc_start: 0.9196 (mmm) cc_final: 0.8869 (mmt) REVERT: B 484 ASP cc_start: 0.7971 (m-30) cc_final: 0.7660 (m-30) REVERT: C 192 GLU cc_start: 0.8167 (pt0) cc_final: 0.7958 (pt0) outliers start: 0 outliers final: 3 residues processed: 218 average time/residue: 1.5318 time to fit residues: 358.7873 Evaluate side-chains 149 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 146 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain C residue 172 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 70 optimal weight: 0.0470 chunk 43 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 0.1980 chunk 97 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN D1004 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.104198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.076235 restraints weight = 19723.697| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.76 r_work: 0.2833 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13145 Z= 0.126 Angle : 0.537 6.424 17817 Z= 0.282 Chirality : 0.043 0.154 2052 Planarity : 0.005 0.067 2366 Dihedral : 4.235 28.380 1843 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.53 % Allowed : 10.48 % Favored : 87.99 % 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: 1.56 (0.21), residues: 1694 helix: 2.12 (0.22), residues: 567 sheet: 1.64 (0.25), residues: 399 loop : -0.18 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 233 HIS 0.003 0.001 HIS C 379 PHE 0.022 0.001 PHE A 493 TYR 0.014 0.001 TYR A 11 ARG 0.008 0.001 ARG A 259 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 748) hydrogen bonds : angle 4.14004 ( 2037) covalent geometry : bond 0.00273 (13145) covalent geometry : angle 0.53728 (17817) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 1.582 Fit side-chains REVERT: A 1 MET cc_start: 0.6716 (pmm) cc_final: 0.6263 (mtt) REVERT: A 19 GLU cc_start: 0.8543 (tt0) cc_final: 0.7834 (tm-30) REVERT: A 389 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7722 (mm-30) REVERT: A 405 ARG cc_start: 0.8013 (tpt-90) cc_final: 0.7542 (tpp80) REVERT: A 512 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8261 (mt-10) REVERT: B 83 ARG cc_start: 0.7477 (ptt180) cc_final: 0.6989 (ppt-90) REVERT: B 484 ASP cc_start: 0.8266 (m-30) cc_final: 0.7989 (m-30) REVERT: C 192 GLU cc_start: 0.8286 (pt0) cc_final: 0.8034 (pt0) REVERT: C 430 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7425 (mp0) outliers start: 21 outliers final: 5 residues processed: 167 average time/residue: 1.3879 time to fit residues: 251.0604 Evaluate side-chains 150 residues out of total 1376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 144 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain D residue 1019 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 59.9706 > 50: distance: 8 - 35: 9.960 distance: 13 - 14: 9.437 distance: 14 - 15: 10.878 distance: 14 - 17: 6.151 distance: 15 - 16: 14.378 distance: 15 - 22: 13.276 distance: 16 - 43: 3.898 distance: 18 - 19: 17.549 distance: 19 - 20: 12.646 distance: 19 - 21: 7.516 distance: 22 - 23: 19.117 distance: 23 - 24: 18.218 distance: 23 - 26: 10.886 distance: 24 - 27: 4.190 distance: 25 - 48: 41.119 distance: 27 - 28: 10.361 distance: 28 - 29: 22.756 distance: 28 - 31: 11.492 distance: 29 - 30: 20.885 distance: 29 - 35: 9.543 distance: 30 - 59: 21.990 distance: 31 - 32: 35.300 distance: 32 - 33: 30.260 distance: 32 - 34: 21.016 distance: 35 - 36: 14.497 distance: 36 - 37: 17.205 distance: 36 - 39: 16.940 distance: 37 - 38: 3.782 distance: 37 - 43: 26.178 distance: 38 - 66: 18.195 distance: 39 - 40: 7.337 distance: 40 - 41: 12.752 distance: 40 - 42: 22.070 distance: 43 - 44: 10.668 distance: 44 - 45: 16.677 distance: 44 - 47: 24.328 distance: 45 - 46: 10.487 distance: 45 - 48: 21.868 distance: 46 - 71: 36.800 distance: 48 - 49: 11.901 distance: 49 - 50: 6.649 distance: 49 - 52: 8.991 distance: 50 - 51: 7.512 distance: 50 - 59: 20.098 distance: 51 - 76: 32.663 distance: 52 - 53: 17.136 distance: 53 - 54: 10.052 distance: 54 - 55: 5.419 distance: 55 - 56: 13.005 distance: 56 - 57: 4.184 distance: 56 - 58: 12.899 distance: 59 - 60: 24.849 distance: 60 - 61: 7.232 distance: 60 - 63: 13.183 distance: 61 - 62: 7.182 distance: 61 - 66: 17.577 distance: 62 - 84: 35.131 distance: 63 - 64: 22.036 distance: 63 - 65: 3.388 distance: 66 - 67: 5.058 distance: 67 - 68: 15.812 distance: 67 - 70: 22.216 distance: 68 - 69: 19.487 distance: 68 - 71: 7.084 distance: 69 - 89: 22.228 distance: 71 - 72: 12.916 distance: 72 - 73: 13.936 distance: 72 - 75: 43.439 distance: 73 - 74: 12.123 distance: 73 - 76: 14.909 distance: 76 - 77: 30.357 distance: 77 - 78: 18.573 distance: 77 - 80: 23.224 distance: 78 - 79: 44.772 distance: 78 - 84: 24.945 distance: 80 - 81: 15.765 distance: 81 - 82: 30.324 distance: 81 - 83: 40.381