Starting phenix.real_space_refine on Tue Jan 21 07:42:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wzh_37952/01_2025/8wzh_37952.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wzh_37952/01_2025/8wzh_37952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wzh_37952/01_2025/8wzh_37952.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wzh_37952/01_2025/8wzh_37952.map" model { file = "/net/cci-nas-00/data/ceres_data/8wzh_37952/01_2025/8wzh_37952.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wzh_37952/01_2025/8wzh_37952.cif" } resolution = 3.7 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= 0.007 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: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 12 5.49 5 S 52 5.16 5 C 10392 2.51 5 N 2884 2.21 5 O 3024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 136 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 16368 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 4001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 4001 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} Chain: "A" Number of atoms: 4001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 4001 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} Chain: "C" Number of atoms: 4001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 4001 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} Chain: "D" Number of atoms: 4001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 4001 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} Chain: "B" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.48, per 1000 atoms: 0.64 Number of scatterers: 16368 At special positions: 0 Unit cell: (110.21, 114.49, 86.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 52 16.00 P 12 15.00 O 3024 8.00 N 2884 7.00 C 10392 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.33 Conformation dependent library (CDL) restraints added in 2.0 seconds 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3712 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 8 sheets defined 40.2% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'B' and resid 6 through 9 Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 54 through 65 removed outlier: 3.685A pdb=" N THR B 58 " --> pdb=" O ASP B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.564A pdb=" N GLU B 101 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 160 through 169 Processing helix chain 'B' and resid 178 through 189 removed outlier: 3.691A pdb=" N VAL B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 200 Processing helix chain 'B' and resid 201 through 205 removed outlier: 4.020A pdb=" N ILE B 205 " --> pdb=" O ASP B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 257 removed outlier: 3.605A pdb=" N GLN B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 285 through 291 Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 348 through 366 removed outlier: 3.629A pdb=" N PHE B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) Proline residue: B 359 - end of helix Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 415 through 419 removed outlier: 3.930A pdb=" N LEU B 419 " --> pdb=" O PRO B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 451 removed outlier: 3.855A pdb=" N LEU B 451 " --> pdb=" O TYR B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 468 Processing helix chain 'B' and resid 471 through 486 Processing helix chain 'B' and resid 486 through 501 Processing helix chain 'A' and resid 6 through 9 Processing helix chain 'A' and resid 10 through 19 Processing helix chain 'A' and resid 54 through 65 removed outlier: 3.683A pdb=" N THR A 58 " --> pdb=" O ASP A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.565A pdb=" N GLU A 101 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 178 through 189 removed outlier: 3.692A pdb=" N VAL A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 200 Processing helix chain 'A' and resid 201 through 205 removed outlier: 4.020A pdb=" N ILE A 205 " --> pdb=" O ASP A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 257 removed outlier: 3.604A pdb=" N GLN A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 272 Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 348 through 366 removed outlier: 3.629A pdb=" N PHE A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Proline residue: A 359 - end of helix Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 415 through 419 removed outlier: 3.930A pdb=" N LEU A 419 " --> pdb=" O PRO A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 removed outlier: 3.856A pdb=" N LEU A 451 " --> pdb=" O TYR A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 468 Processing helix chain 'A' and resid 471 through 486 Processing helix chain 'A' and resid 486 through 501 Processing helix chain 'C' and resid 6 through 9 Processing helix chain 'C' and resid 10 through 19 Processing helix chain 'C' and resid 54 through 65 removed outlier: 3.685A pdb=" N THR C 58 " --> pdb=" O ASP C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.564A pdb=" N GLU C 101 " --> pdb=" O LYS C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'C' and resid 160 through 169 Processing helix chain 'C' and resid 178 through 189 removed outlier: 3.692A pdb=" N VAL C 182 " --> pdb=" O ASP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 200 Processing helix chain 'C' and resid 201 through 205 removed outlier: 4.020A pdb=" N ILE C 205 " --> pdb=" O ASP C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 257 removed outlier: 3.605A pdb=" N GLN C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 272 Processing helix chain 'C' and resid 285 through 291 Processing helix chain 'C' and resid 324 through 330 Processing helix chain 'C' and resid 348 through 366 removed outlier: 3.628A pdb=" N PHE C 356 " --> pdb=" O GLN C 352 " (cutoff:3.500A) Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 369 through 373 Processing helix chain 'C' and resid 415 through 419 removed outlier: 3.930A pdb=" N LEU C 419 " --> pdb=" O PRO C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 451 removed outlier: 3.856A pdb=" N LEU C 451 " --> pdb=" O TYR C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 468 Processing helix chain 'C' and resid 471 through 486 Processing helix chain 'C' and resid 486 through 501 Processing helix chain 'D' and resid 6 through 9 Processing helix chain 'D' and resid 10 through 19 Processing helix chain 'D' and resid 54 through 65 removed outlier: 3.683A pdb=" N THR D 58 " --> pdb=" O ASP D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.564A pdb=" N GLU D 101 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 159 No H-bonds generated for 'chain 'D' and resid 157 through 159' Processing helix chain 'D' and resid 160 through 169 Processing helix chain 'D' and resid 178 through 189 removed outlier: 3.692A pdb=" N VAL D 182 " --> pdb=" O ASP D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 200 Processing helix chain 'D' and resid 201 through 205 removed outlier: 4.020A pdb=" N ILE D 205 " --> pdb=" O ASP D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 257 removed outlier: 3.605A pdb=" N GLN D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 272 Processing helix chain 'D' and resid 285 through 291 Processing helix chain 'D' and resid 324 through 330 Processing helix chain 'D' and resid 348 through 366 removed outlier: 3.628A pdb=" N PHE D 356 " --> pdb=" O GLN D 352 " (cutoff:3.500A) Proline residue: D 359 - end of helix Processing helix chain 'D' and resid 369 through 373 Processing helix chain 'D' and resid 415 through 419 removed outlier: 3.930A pdb=" N LEU D 419 " --> pdb=" O PRO D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 451 removed outlier: 3.856A pdb=" N LEU D 451 " --> pdb=" O TYR D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 468 Processing helix chain 'D' and resid 471 through 486 Processing helix chain 'D' and resid 486 through 501 Processing sheet with id=AA1, first strand: chain 'B' and resid 42 through 44 removed outlier: 3.738A pdb=" N ARG D 430 " --> pdb=" O THR B 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 343 through 344 removed outlier: 3.678A pdb=" N GLY B 314 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE B 281 " --> pdb=" O PRO B 312 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU B 316 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N GLU B 86 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU B 318 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N TYR B 84 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 429 through 431 removed outlier: 3.532A pdb=" N ARG B 430 " --> pdb=" O THR D 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 42 through 44 removed outlier: 3.507A pdb=" N ARG C 430 " --> pdb=" O THR A 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 344 removed outlier: 3.678A pdb=" N GLY A 314 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE A 281 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU A 316 " --> pdb=" O GLU A 86 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N GLU A 86 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU A 318 " --> pdb=" O TYR A 84 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N TYR A 84 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 429 through 431 removed outlier: 3.627A pdb=" N ARG A 430 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 343 through 344 removed outlier: 3.678A pdb=" N GLY C 314 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE C 281 " --> pdb=" O PRO C 312 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU C 316 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N GLU C 86 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LEU C 318 " --> pdb=" O TYR C 84 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N TYR C 84 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 343 through 344 removed outlier: 3.679A pdb=" N GLY D 314 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE D 281 " --> pdb=" O PRO D 312 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU D 316 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLU D 86 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU D 318 " --> pdb=" O TYR D 84 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N TYR D 84 " --> pdb=" O LEU D 318 " (cutoff:3.500A) 647 hydrogen bonds defined for protein. 1833 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: 4.89 Time building geometry restraints manager: 4.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 6843 1.39 - 1.57: 9921 1.57 - 1.75: 20 1.75 - 1.93: 92 1.93 - 2.11: 12 Bond restraints: 16888 Sorted by residual: bond pdb=" O2B NDP D3002 " pdb=" P2B NDP D3002 " ideal model delta sigma weight residual 1.833 1.616 0.217 3.80e-02 6.93e+02 3.26e+01 bond pdb=" O2B NDP B3002 " pdb=" P2B NDP B3002 " ideal model delta sigma weight residual 1.833 1.616 0.217 3.80e-02 6.93e+02 3.25e+01 bond pdb=" O2B NDP A3002 " pdb=" P2B NDP A3002 " ideal model delta sigma weight residual 1.833 1.617 0.216 3.80e-02 6.93e+02 3.23e+01 bond pdb=" O2B NDP C3002 " pdb=" P2B NDP C3002 " ideal model delta sigma weight residual 1.833 1.617 0.216 3.80e-02 6.93e+02 3.23e+01 bond pdb=" O5D NDP A3002 " pdb=" PN NDP A3002 " ideal model delta sigma weight residual 1.757 1.589 0.168 3.50e-02 8.16e+02 2.30e+01 ... (remaining 16883 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 19711 2.03 - 4.06: 3203 4.06 - 6.09: 94 6.09 - 8.12: 20 8.12 - 10.15: 12 Bond angle restraints: 23040 Sorted by residual: angle pdb=" O1X NDP A3002 " pdb=" P2B NDP A3002 " pdb=" O3X NDP A3002 " ideal model delta sigma weight residual 117.46 111.91 5.55 1.17e+00 7.36e-01 2.26e+01 angle pdb=" O1X NDP D3002 " pdb=" P2B NDP D3002 " pdb=" O3X NDP D3002 " ideal model delta sigma weight residual 117.46 111.96 5.50 1.17e+00 7.36e-01 2.23e+01 angle pdb=" O1X NDP B3002 " pdb=" P2B NDP B3002 " pdb=" O3X NDP B3002 " ideal model delta sigma weight residual 117.46 111.97 5.49 1.17e+00 7.36e-01 2.22e+01 angle pdb=" O1X NDP C3002 " pdb=" P2B NDP C3002 " pdb=" O3X NDP C3002 " ideal model delta sigma weight residual 117.46 112.02 5.44 1.17e+00 7.36e-01 2.18e+01 angle pdb=" O2B NDP B3002 " pdb=" P2B NDP B3002 " pdb=" O3X NDP B3002 " ideal model delta sigma weight residual 97.70 107.85 -10.15 2.45e+00 1.67e-01 1.72e+01 ... (remaining 23035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 8836 17.89 - 35.78: 776 35.78 - 53.67: 148 53.67 - 71.56: 76 71.56 - 89.45: 24 Dihedral angle restraints: 9860 sinusoidal: 4080 harmonic: 5780 Sorted by residual: dihedral pdb=" CA ASN D 439 " pdb=" C ASN D 439 " pdb=" N VAL D 440 " pdb=" CA VAL D 440 " ideal model delta harmonic sigma weight residual -180.00 -161.46 -18.54 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ASN A 439 " pdb=" C ASN A 439 " pdb=" N VAL A 440 " pdb=" CA VAL A 440 " ideal model delta harmonic sigma weight residual 180.00 -161.46 -18.54 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ASN B 439 " pdb=" C ASN B 439 " pdb=" N VAL B 440 " pdb=" CA VAL B 440 " ideal model delta harmonic sigma weight residual -180.00 -161.48 -18.52 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 9857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 960 0.040 - 0.079: 701 0.079 - 0.119: 480 0.119 - 0.159: 167 0.159 - 0.198: 20 Chirality restraints: 2328 Sorted by residual: chirality pdb=" C4D NDP D3002 " pdb=" C3D NDP D3002 " pdb=" C5D NDP D3002 " pdb=" O4D NDP D3002 " both_signs ideal model delta sigma weight residual False -2.71 -2.52 -0.20 2.00e-01 2.50e+01 9.84e-01 chirality pdb=" C4D NDP C3002 " pdb=" C3D NDP C3002 " pdb=" C5D NDP C3002 " pdb=" O4D NDP C3002 " both_signs ideal model delta sigma weight residual False -2.71 -2.52 -0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" C4D NDP A3002 " pdb=" C3D NDP A3002 " pdb=" C5D NDP A3002 " pdb=" O4D NDP A3002 " both_signs ideal model delta sigma weight residual False -2.71 -2.52 -0.20 2.00e-01 2.50e+01 9.72e-01 ... (remaining 2325 not shown) Planarity restraints: 3052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB HEM B3001 " -0.011 2.00e-02 2.50e+03 1.34e-02 4.02e+00 pdb=" C1B HEM B3001 " 0.004 2.00e-02 2.50e+03 pdb=" C2B HEM B3001 " -0.001 2.00e-02 2.50e+03 pdb=" C3B HEM B3001 " 0.003 2.00e-02 2.50e+03 pdb=" C4B HEM B3001 " -0.014 2.00e-02 2.50e+03 pdb=" CAB HEM B3001 " 0.020 2.00e-02 2.50e+03 pdb=" CHB HEM B3001 " 0.021 2.00e-02 2.50e+03 pdb=" CHC HEM B3001 " 0.000 2.00e-02 2.50e+03 pdb=" CMB HEM B3001 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEM A3001 " -0.011 2.00e-02 2.50e+03 1.34e-02 4.02e+00 pdb=" C1B HEM A3001 " 0.003 2.00e-02 2.50e+03 pdb=" C2B HEM A3001 " -0.001 2.00e-02 2.50e+03 pdb=" C3B HEM A3001 " 0.003 2.00e-02 2.50e+03 pdb=" C4B HEM A3001 " -0.014 2.00e-02 2.50e+03 pdb=" CAB HEM A3001 " 0.020 2.00e-02 2.50e+03 pdb=" CHB HEM A3001 " 0.021 2.00e-02 2.50e+03 pdb=" CHC HEM A3001 " -0.000 2.00e-02 2.50e+03 pdb=" CMB HEM A3001 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEM C3001 " 0.012 2.00e-02 2.50e+03 1.31e-02 3.88e+00 pdb=" C1B HEM C3001 " -0.003 2.00e-02 2.50e+03 pdb=" C2B HEM C3001 " 0.001 2.00e-02 2.50e+03 pdb=" C3B HEM C3001 " -0.003 2.00e-02 2.50e+03 pdb=" C4B HEM C3001 " 0.013 2.00e-02 2.50e+03 pdb=" CAB HEM C3001 " -0.019 2.00e-02 2.50e+03 pdb=" CHB HEM C3001 " -0.021 2.00e-02 2.50e+03 pdb=" CHC HEM C3001 " 0.000 2.00e-02 2.50e+03 pdb=" CMB HEM C3001 " 0.021 2.00e-02 2.50e+03 ... (remaining 3049 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3826 2.83 - 3.35: 16437 3.35 - 3.86: 26663 3.86 - 4.38: 32562 4.38 - 4.90: 54551 Nonbonded interactions: 134039 Sorted by model distance: nonbonded pdb=" OH TYR A 137 " pdb=" O VAL A 375 " model vdw 2.311 3.040 nonbonded pdb=" OH TYR C 137 " pdb=" O VAL C 375 " model vdw 2.311 3.040 nonbonded pdb=" OH TYR D 137 " pdb=" O VAL D 375 " model vdw 2.311 3.040 nonbonded pdb=" OH TYR B 137 " pdb=" O VAL B 375 " model vdw 2.311 3.040 nonbonded pdb=" O LEU A 451 " pdb=" NH2 ARG A 456 " model vdw 2.318 3.120 ... (remaining 134034 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.320 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: 0.000 Set scattering table: 0.000 Process input model: 36.810 Find NCS groups from input model: 0.320 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: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 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 : 0.013 0.217 16888 Z= 0.873 Angle : 1.375 10.147 23040 Z= 0.981 Chirality : 0.070 0.198 2328 Planarity : 0.004 0.018 3052 Dihedral : 15.634 89.449 6148 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.93 % Allowed : 3.74 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -2.69 (0.16), residues: 1980 helix: -1.14 (0.17), residues: 676 sheet: -1.12 (0.28), residues: 220 loop : -2.43 (0.16), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 183 HIS 0.008 0.003 HIS C 166 PHE 0.020 0.003 PHE C 356 TYR 0.022 0.003 TYR C 489 ARG 0.005 0.001 ARG D 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 1.952 Fit side-chains revert: symmetry clash REVERT: B 59 ASP cc_start: 0.7180 (m-30) cc_final: 0.6839 (m-30) REVERT: B 119 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: B 259 ASP cc_start: 0.8290 (p0) cc_final: 0.7653 (p0) REVERT: B 260 TYR cc_start: 0.7497 (t80) cc_final: 0.7095 (t80) REVERT: B 321 ASN cc_start: 0.8352 (m-40) cc_final: 0.8136 (m-40) REVERT: B 330 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7934 (mm-30) REVERT: A 119 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: A 259 ASP cc_start: 0.8077 (p0) cc_final: 0.7397 (p0) REVERT: A 330 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7922 (mm-30) REVERT: A 339 MET cc_start: 0.8073 (mtm) cc_final: 0.7856 (mtm) REVERT: C 59 ASP cc_start: 0.7099 (m-30) cc_final: 0.6725 (m-30) REVERT: C 119 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: C 259 ASP cc_start: 0.8260 (p0) cc_final: 0.7599 (p0) REVERT: C 260 TYR cc_start: 0.7509 (t80) cc_final: 0.7108 (t80) REVERT: C 321 ASN cc_start: 0.8343 (m-40) cc_final: 0.8129 (m-40) REVERT: C 330 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7927 (mm-30) REVERT: C 339 MET cc_start: 0.8066 (mtm) cc_final: 0.7860 (mtm) REVERT: D 119 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: D 259 ASP cc_start: 0.8179 (p0) cc_final: 0.7496 (p0) REVERT: D 330 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7869 (mm-30) outliers start: 16 outliers final: 4 residues processed: 217 average time/residue: 0.2994 time to fit residues: 96.8977 Evaluate side-chains 154 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 440 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.9990 chunk 148 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 153 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 177 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 HIS B 148 ASN B 282 GLN B 331 GLN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 89 HIS A 282 GLN A 331 GLN ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 HIS C 282 GLN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 HIS D 282 GLN D 331 GLN ** D 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.111941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.087106 restraints weight = 25587.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.089761 restraints weight = 16073.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.091521 restraints weight = 12023.255| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16888 Z= 0.218 Angle : 0.547 4.775 23040 Z= 0.280 Chirality : 0.043 0.134 2328 Planarity : 0.004 0.039 3052 Dihedral : 8.498 93.722 2268 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.57 % Allowed : 8.00 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.77 (0.18), residues: 1980 helix: 0.73 (0.20), residues: 684 sheet: -0.13 (0.28), residues: 272 loop : -1.52 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 183 HIS 0.004 0.001 HIS C 364 PHE 0.020 0.002 PHE A 132 TYR 0.017 0.001 TYR A 489 ARG 0.003 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 170 time to evaluate : 1.812 Fit side-chains REVERT: B 60 GLU cc_start: 0.7790 (tp30) cc_final: 0.7585 (tp30) REVERT: B 259 ASP cc_start: 0.7309 (p0) cc_final: 0.6887 (p0) REVERT: B 321 ASN cc_start: 0.8814 (m-40) cc_final: 0.8571 (m-40) REVERT: B 394 MET cc_start: 0.6586 (tmm) cc_final: 0.5974 (ttt) REVERT: A 259 ASP cc_start: 0.7260 (p0) cc_final: 0.6847 (p0) REVERT: C 26 VAL cc_start: 0.7518 (OUTLIER) cc_final: 0.7300 (p) REVERT: C 60 GLU cc_start: 0.7858 (tp30) cc_final: 0.7653 (tp30) REVERT: C 259 ASP cc_start: 0.7276 (p0) cc_final: 0.6793 (p0) REVERT: C 321 ASN cc_start: 0.8835 (m-40) cc_final: 0.8616 (m-40) REVERT: D 259 ASP cc_start: 0.7322 (p0) cc_final: 0.6860 (p0) outliers start: 44 outliers final: 25 residues processed: 189 average time/residue: 0.2505 time to fit residues: 74.7716 Evaluate side-chains 163 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 2.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 440 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 32 optimal weight: 4.9990 chunk 34 optimal weight: 0.0060 chunk 50 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 179 optimal weight: 4.9990 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 407 ASN A 407 ASN C 331 GLN C 407 ASN D 407 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.110792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.086510 restraints weight = 25652.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.089079 restraints weight = 15798.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.090764 restraints weight = 11821.125| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16888 Z= 0.235 Angle : 0.539 5.279 23040 Z= 0.274 Chirality : 0.043 0.136 2328 Planarity : 0.004 0.044 3052 Dihedral : 7.822 90.916 2256 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.57 % Allowed : 9.35 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.33 (0.18), residues: 1980 helix: 1.14 (0.20), residues: 684 sheet: 0.13 (0.29), residues: 272 loop : -1.30 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 183 HIS 0.004 0.001 HIS A 235 PHE 0.023 0.002 PHE B 100 TYR 0.015 0.001 TYR A 489 ARG 0.002 0.000 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 156 time to evaluate : 1.945 Fit side-chains REVERT: B 259 ASP cc_start: 0.7297 (p0) cc_final: 0.6907 (p0) REVERT: B 321 ASN cc_start: 0.8837 (m-40) cc_final: 0.8564 (m-40) REVERT: A 259 ASP cc_start: 0.7265 (p0) cc_final: 0.6730 (p0) REVERT: A 321 ASN cc_start: 0.8873 (m-40) cc_final: 0.8589 (m-40) REVERT: C 259 ASP cc_start: 0.7334 (p0) cc_final: 0.6906 (p0) REVERT: C 321 ASN cc_start: 0.8876 (m-40) cc_final: 0.8614 (m-40) REVERT: C 394 MET cc_start: 0.7763 (mmt) cc_final: 0.7438 (mmt) REVERT: D 236 TYR cc_start: 0.8920 (OUTLIER) cc_final: 0.8709 (p90) REVERT: D 259 ASP cc_start: 0.7314 (p0) cc_final: 0.6856 (p0) REVERT: D 494 GLN cc_start: 0.8070 (tp-100) cc_final: 0.7684 (tp-100) outliers start: 44 outliers final: 28 residues processed: 179 average time/residue: 0.2834 time to fit residues: 81.3790 Evaluate side-chains 169 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 497 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 61 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 40 optimal weight: 0.0980 chunk 135 optimal weight: 0.9980 chunk 189 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.110493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.086057 restraints weight = 25808.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.088689 restraints weight = 16119.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.090411 restraints weight = 12053.103| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 16888 Z= 0.291 Angle : 0.554 4.806 23040 Z= 0.283 Chirality : 0.044 0.135 2328 Planarity : 0.004 0.048 3052 Dihedral : 7.805 89.025 2253 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.92 % Allowed : 10.22 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.22 (0.18), residues: 1980 helix: 1.24 (0.20), residues: 684 sheet: 0.20 (0.29), residues: 272 loop : -1.23 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 183 HIS 0.004 0.001 HIS C 362 PHE 0.029 0.002 PHE C 100 TYR 0.015 0.001 TYR D 489 ARG 0.003 0.000 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 151 time to evaluate : 1.819 Fit side-chains revert: symmetry clash REVERT: B 259 ASP cc_start: 0.7271 (p0) cc_final: 0.6857 (p0) REVERT: B 321 ASN cc_start: 0.8851 (m-40) cc_final: 0.8588 (m-40) REVERT: B 500 TYR cc_start: 0.7074 (OUTLIER) cc_final: 0.6653 (m-80) REVERT: A 259 ASP cc_start: 0.7149 (p0) cc_final: 0.6726 (p0) REVERT: A 494 GLN cc_start: 0.8076 (tp-100) cc_final: 0.7701 (tp-100) REVERT: A 500 TYR cc_start: 0.7089 (OUTLIER) cc_final: 0.6687 (m-80) REVERT: C 259 ASP cc_start: 0.7281 (p0) cc_final: 0.6869 (p0) REVERT: C 321 ASN cc_start: 0.8867 (m-40) cc_final: 0.8601 (m-40) REVERT: C 394 MET cc_start: 0.7656 (mmt) cc_final: 0.7182 (mmt) REVERT: D 259 ASP cc_start: 0.7302 (p0) cc_final: 0.6864 (p0) REVERT: D 321 ASN cc_start: 0.8862 (m-40) cc_final: 0.8593 (m-40) REVERT: D 500 TYR cc_start: 0.7143 (OUTLIER) cc_final: 0.6729 (m-80) outliers start: 50 outliers final: 26 residues processed: 181 average time/residue: 0.2553 time to fit residues: 73.0798 Evaluate side-chains 173 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 2.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 500 TYR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 500 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 45 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 159 optimal weight: 0.9990 chunk 186 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 148 optimal weight: 10.0000 chunk 181 optimal weight: 0.1980 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 471 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.112223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.087928 restraints weight = 26036.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.090557 restraints weight = 16115.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.092314 restraints weight = 12024.152| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 16888 Z= 0.316 Angle : 0.580 9.673 23040 Z= 0.293 Chirality : 0.045 0.138 2328 Planarity : 0.004 0.051 3052 Dihedral : 7.803 87.298 2252 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.86 % Allowed : 10.86 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.19 (0.18), residues: 1980 helix: 1.24 (0.20), residues: 684 sheet: 0.21 (0.29), residues: 272 loop : -1.20 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 183 HIS 0.004 0.001 HIS C 362 PHE 0.029 0.002 PHE A 100 TYR 0.015 0.001 TYR A 489 ARG 0.003 0.000 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 155 time to evaluate : 1.847 Fit side-chains REVERT: B 259 ASP cc_start: 0.7203 (p0) cc_final: 0.6829 (p0) REVERT: B 321 ASN cc_start: 0.8849 (m-40) cc_final: 0.8596 (m-40) REVERT: B 500 TYR cc_start: 0.7155 (OUTLIER) cc_final: 0.6645 (m-80) REVERT: A 259 ASP cc_start: 0.7123 (p0) cc_final: 0.6735 (p0) REVERT: A 500 TYR cc_start: 0.7120 (OUTLIER) cc_final: 0.6674 (m-80) REVERT: C 259 ASP cc_start: 0.7266 (p0) cc_final: 0.6837 (p0) REVERT: C 321 ASN cc_start: 0.8893 (m-40) cc_final: 0.8640 (m-40) REVERT: C 394 MET cc_start: 0.7593 (mmt) cc_final: 0.6767 (mmm) REVERT: C 500 TYR cc_start: 0.7191 (OUTLIER) cc_final: 0.6657 (m-80) REVERT: D 259 ASP cc_start: 0.7269 (p0) cc_final: 0.6855 (p0) REVERT: D 321 ASN cc_start: 0.8882 (m-40) cc_final: 0.8587 (m-40) REVERT: D 494 GLN cc_start: 0.7940 (tp-100) cc_final: 0.7616 (tp-100) REVERT: D 500 TYR cc_start: 0.7203 (OUTLIER) cc_final: 0.6753 (m-80) outliers start: 49 outliers final: 34 residues processed: 186 average time/residue: 0.2731 time to fit residues: 78.4288 Evaluate side-chains 184 residues out of total 1712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 500 TYR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 198 PHE Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 500 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- 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: 62.2852 > 50: distance: 68 - 73: 22.385 distance: 73 - 74: 29.348 distance: 74 - 75: 9.453 distance: 74 - 77: 33.438 distance: 75 - 76: 21.819 distance: 75 - 85: 21.404 distance: 77 - 78: 39.828 distance: 78 - 79: 32.876 distance: 78 - 80: 18.311 distance: 79 - 81: 33.348 distance: 80 - 82: 20.983 distance: 81 - 83: 3.353 distance: 82 - 83: 24.021 distance: 83 - 84: 25.192 distance: 85 - 86: 35.874 distance: 86 - 87: 39.664 distance: 86 - 89: 19.241 distance: 87 - 88: 47.367 distance: 87 - 97: 28.154 distance: 89 - 90: 8.792 distance: 90 - 91: 21.557 distance: 90 - 92: 17.333 distance: 91 - 93: 15.053 distance: 92 - 94: 19.981 distance: 93 - 95: 13.476 distance: 94 - 95: 14.018 distance: 95 - 96: 32.190 distance: 97 - 98: 14.715 distance: 97 - 103: 49.467 distance: 98 - 99: 45.307 distance: 98 - 101: 43.772 distance: 99 - 100: 16.636 distance: 99 - 104: 8.396 distance: 101 - 102: 40.853 distance: 102 - 103: 19.279 distance: 104 - 105: 11.773 distance: 105 - 106: 26.910 distance: 105 - 108: 7.723 distance: 106 - 107: 31.722 distance: 106 - 112: 29.429 distance: 108 - 109: 22.004 distance: 109 - 110: 3.393 distance: 109 - 111: 8.885 distance: 112 - 113: 28.744 distance: 113 - 114: 14.728 distance: 113 - 116: 41.332 distance: 114 - 115: 21.077 distance: 114 - 118: 38.823 distance: 116 - 117: 43.401 distance: 118 - 119: 27.025 distance: 119 - 120: 11.593 distance: 119 - 122: 27.758 distance: 120 - 121: 11.738 distance: 120 - 129: 23.708 distance: 122 - 123: 19.050 distance: 123 - 124: 19.700 distance: 123 - 125: 11.600 distance: 124 - 126: 22.534 distance: 125 - 127: 19.713 distance: 126 - 128: 17.611 distance: 127 - 128: 12.589 distance: 129 - 130: 33.597 distance: 130 - 131: 15.567 distance: 131 - 132: 17.588 distance: 131 - 133: 9.995 distance: 133 - 134: 12.341 distance: 134 - 135: 18.956 distance: 134 - 137: 30.109 distance: 135 - 136: 13.231 distance: 135 - 138: 22.402 distance: 138 - 139: 33.763 distance: 138 - 144: 22.096 distance: 139 - 140: 27.182 distance: 139 - 142: 36.888 distance: 140 - 141: 16.259 distance: 140 - 145: 19.997 distance: 142 - 143: 20.443 distance: 143 - 144: 16.141 distance: 145 - 146: 14.289 distance: 146 - 147: 7.011 distance: 146 - 149: 10.892 distance: 147 - 148: 6.853 distance: 147 - 154: 6.292 distance: 149 - 150: 6.660 distance: 150 - 151: 14.588 distance: 151 - 152: 11.064 distance: 151 - 153: 5.734