Starting phenix.real_space_refine on Fri Aug 2 20:24:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2g_35949/08_2024/8j2g_35949.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2g_35949/08_2024/8j2g_35949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2g_35949/08_2024/8j2g_35949.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2g_35949/08_2024/8j2g_35949.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2g_35949/08_2024/8j2g_35949.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j2g_35949/08_2024/8j2g_35949.cif" } resolution = 3.4 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= 0.010 sd= 0.143 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 42 5.16 5 C 3282 2.51 5 N 860 2.21 5 O 874 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 6": "NH1" <-> "NH2" Residue "B ARG 6": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 5058 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2529 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 313} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2529 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 313} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 3.43, per 1000 atoms: 0.68 Number of scatterers: 5058 At special positions: 0 Unit cell: (73.7, 67.1, 126.5, 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 42 16.00 O 874 8.00 N 860 7.00 C 3282 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 282 " distance=2.03 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 282 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 891.7 milliseconds 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1216 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 2 sheets defined 45.5% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 11 through 32 removed outlier: 3.658A pdb=" N LEU A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N MET A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 23 " --> pdb=" O PHE A 19 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.716A pdb=" N LEU A 45 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER A 46 " --> pdb=" O HIS A 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 42 through 46' Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.905A pdb=" N GLU A 58 " --> pdb=" O ALA A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 85 removed outlier: 3.591A pdb=" N VAL A 84 " --> pdb=" O MET A 80 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 80 through 85' Processing helix chain 'A' and resid 94 through 100 Processing helix chain 'A' and resid 101 through 106 removed outlier: 3.859A pdb=" N ILE A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 125 removed outlier: 3.540A pdb=" N VAL A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA A 122 " --> pdb=" O GLY A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 removed outlier: 3.963A pdb=" N LEU A 131 " --> pdb=" O ASN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 254 Processing helix chain 'A' and resid 260 through 272 removed outlier: 3.521A pdb=" N LEU A 267 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 315 removed outlier: 3.628A pdb=" N LEU A 314 " --> pdb=" O CYS A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 324 removed outlier: 3.680A pdb=" N CYS A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL A 322 " --> pdb=" O PRO A 318 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 323 " --> pdb=" O THR A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 332 removed outlier: 4.094A pdb=" N TYR A 330 " --> pdb=" O CYS A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 339 removed outlier: 3.864A pdb=" N GLU A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 355 removed outlier: 3.579A pdb=" N ASN A 355 " --> pdb=" O ASP A 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 355' Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.694A pdb=" N ARG A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'B' and resid 11 through 32 removed outlier: 3.659A pdb=" N LEU B 15 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N MET B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 23 " --> pdb=" O PHE B 19 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.716A pdb=" N LEU B 45 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER B 46 " --> pdb=" O HIS B 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 42 through 46' Processing helix chain 'B' and resid 48 through 51 Processing helix chain 'B' and resid 52 through 61 removed outlier: 3.904A pdb=" N GLU B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.592A pdb=" N VAL B 84 " --> pdb=" O MET B 80 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 80 through 85' Processing helix chain 'B' and resid 94 through 100 Processing helix chain 'B' and resid 101 through 106 removed outlier: 3.858A pdb=" N ILE B 105 " --> pdb=" O ILE B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 125 removed outlier: 3.539A pdb=" N VAL B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA B 122 " --> pdb=" O GLY B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 131 removed outlier: 3.964A pdb=" N LEU B 131 " --> pdb=" O ASN B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 254 Processing helix chain 'B' and resid 260 through 272 removed outlier: 3.522A pdb=" N LEU B 267 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 315 removed outlier: 3.627A pdb=" N LEU B 314 " --> pdb=" O CYS B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 324 removed outlier: 3.680A pdb=" N CYS B 321 " --> pdb=" O ASP B 317 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL B 322 " --> pdb=" O PRO B 318 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 323 " --> pdb=" O THR B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 332 removed outlier: 4.093A pdb=" N TYR B 330 " --> pdb=" O CYS B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 339 removed outlier: 3.864A pdb=" N GLU B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 355 removed outlier: 3.580A pdb=" N ASN B 355 " --> pdb=" O ASP B 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 355' Processing helix chain 'B' and resid 356 through 361 removed outlier: 3.694A pdb=" N ARG B 361 " --> pdb=" O ILE B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 409 Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 376 removed outlier: 6.697A pdb=" N VAL A 369 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LYS A 389 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N GLU A 371 " --> pdb=" O HIS A 387 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS A 387 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA A 414 " --> pdb=" O ILE A 382 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 368 through 376 removed outlier: 6.697A pdb=" N VAL B 369 " --> pdb=" O LYS B 389 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N LYS B 389 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N GLU B 371 " --> pdb=" O HIS B 387 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS B 387 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA B 414 " --> pdb=" O ILE B 382 " (cutoff:3.500A) 128 hydrogen bonds defined for protein. 372 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: 1.11 Time building geometry restraints manager: 1.93 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: 1588 1.34 - 1.46: 950 1.46 - 1.58: 2572 1.58 - 1.70: 0 1.70 - 1.81: 62 Bond restraints: 5172 Sorted by residual: bond pdb=" CA HIS B 251 " pdb=" C HIS B 251 " ideal model delta sigma weight residual 1.523 1.463 0.060 1.56e-02 4.11e+03 1.50e+01 bond pdb=" CA HIS A 251 " pdb=" C HIS A 251 " ideal model delta sigma weight residual 1.523 1.463 0.060 1.56e-02 4.11e+03 1.50e+01 bond pdb=" CB PRO A 318 " pdb=" CG PRO A 318 " ideal model delta sigma weight residual 1.492 1.388 0.104 5.00e-02 4.00e+02 4.34e+00 bond pdb=" CB PRO B 318 " pdb=" CG PRO B 318 " ideal model delta sigma weight residual 1.492 1.388 0.104 5.00e-02 4.00e+02 4.29e+00 bond pdb=" CB VAL B 248 " pdb=" CG1 VAL B 248 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.76e+00 ... (remaining 5167 not shown) Histogram of bond angle deviations from ideal: 96.64 - 104.15: 70 104.15 - 111.66: 2315 111.66 - 119.17: 1981 119.17 - 126.68: 2575 126.68 - 134.19: 93 Bond angle restraints: 7034 Sorted by residual: angle pdb=" N ARG B 246 " pdb=" CA ARG B 246 " pdb=" C ARG B 246 " ideal model delta sigma weight residual 114.64 102.81 11.83 1.52e+00 4.33e-01 6.06e+01 angle pdb=" N ARG A 246 " pdb=" CA ARG A 246 " pdb=" C ARG A 246 " ideal model delta sigma weight residual 114.64 102.86 11.78 1.52e+00 4.33e-01 6.01e+01 angle pdb=" N LEU A 45 " pdb=" CA LEU A 45 " pdb=" C LEU A 45 " ideal model delta sigma weight residual 114.12 108.34 5.78 1.39e+00 5.18e-01 1.73e+01 angle pdb=" N LEU B 45 " pdb=" CA LEU B 45 " pdb=" C LEU B 45 " ideal model delta sigma weight residual 114.12 108.39 5.73 1.39e+00 5.18e-01 1.70e+01 angle pdb=" C PHE A 134 " pdb=" N HIS A 135 " pdb=" CA HIS A 135 " ideal model delta sigma weight residual 120.82 126.73 -5.91 1.47e+00 4.63e-01 1.62e+01 ... (remaining 7029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.99: 2399 7.99 - 15.99: 455 15.99 - 23.98: 117 23.98 - 31.98: 39 31.98 - 39.97: 30 Dihedral angle restraints: 3040 sinusoidal: 1166 harmonic: 1874 Sorted by residual: dihedral pdb=" CA ASN B 299 " pdb=" C ASN B 299 " pdb=" N SER B 300 " pdb=" CA SER B 300 " ideal model delta harmonic sigma weight residual -180.00 -147.40 -32.60 0 5.00e+00 4.00e-02 4.25e+01 dihedral pdb=" CA ASN A 299 " pdb=" C ASN A 299 " pdb=" N SER A 300 " pdb=" CA SER A 300 " ideal model delta harmonic sigma weight residual -180.00 -147.46 -32.54 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CA VAL B 128 " pdb=" C VAL B 128 " pdb=" N LEU B 129 " pdb=" CA LEU B 129 " ideal model delta harmonic sigma weight residual 180.00 152.73 27.27 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 3037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 363 0.036 - 0.073: 335 0.073 - 0.109: 98 0.109 - 0.145: 27 0.145 - 0.182: 15 Chirality restraints: 838 Sorted by residual: chirality pdb=" CA PRO A 318 " pdb=" N PRO A 318 " pdb=" C PRO A 318 " pdb=" CB PRO A 318 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.24e-01 chirality pdb=" CA PRO B 318 " pdb=" N PRO B 318 " pdb=" C PRO B 318 " pdb=" CB PRO B 318 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.20e-01 chirality pdb=" CG LEU B 35 " pdb=" CB LEU B 35 " pdb=" CD1 LEU B 35 " pdb=" CD2 LEU B 35 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.93e-01 ... (remaining 835 not shown) Planarity restraints: 878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 317 " 0.048 5.00e-02 4.00e+02 7.21e-02 8.31e+00 pdb=" N PRO B 318 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 318 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 318 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 317 " -0.048 5.00e-02 4.00e+02 7.20e-02 8.30e+00 pdb=" N PRO A 318 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 318 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 318 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 333 " 0.042 5.00e-02 4.00e+02 6.25e-02 6.25e+00 pdb=" N PRO A 334 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 334 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 334 " 0.035 5.00e-02 4.00e+02 ... (remaining 875 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 1797 2.88 - 3.39: 4412 3.39 - 3.89: 7453 3.89 - 4.40: 8331 4.40 - 4.90: 14363 Nonbonded interactions: 36356 Sorted by model distance: nonbonded pdb=" OE2 GLU B 109 " pdb=" NE1 TRP B 273 " model vdw 2.380 3.120 nonbonded pdb=" OE2 GLU A 109 " pdb=" NE1 TRP A 273 " model vdw 2.381 3.120 nonbonded pdb=" NE2 GLN B 376 " pdb=" O GLY B 379 " model vdw 2.382 3.120 nonbonded pdb=" NE2 GLN A 376 " pdb=" O GLY A 379 " model vdw 2.382 3.120 nonbonded pdb=" O GLU B 58 " pdb=" NH1 ARG B 62 " model vdw 2.390 3.120 ... (remaining 36351 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.310 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 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 : 0.010 0.104 5172 Z= 0.616 Angle : 1.138 11.829 7034 Z= 0.625 Chirality : 0.057 0.182 838 Planarity : 0.008 0.072 878 Dihedral : 10.183 38.574 1818 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -6.39 (0.24), residues: 642 helix: -5.04 (0.09), residues: 350 sheet: -1.22 (0.89), residues: 46 loop : -3.27 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 375 HIS 0.008 0.002 HIS B 373 PHE 0.022 0.003 PHE A 407 TYR 0.012 0.003 TYR B 270 ARG 0.011 0.001 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8090 (ttp-170) cc_final: 0.7886 (ttp-110) REVERT: A 99 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7481 (tm-30) REVERT: B 64 THR cc_start: 0.8794 (p) cc_final: 0.8353 (m) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1642 time to fit residues: 21.2627 Evaluate side-chains 76 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 HIS A 370 HIS A 409 ASN A 413 HIS B 251 HIS B 284 ASN B 370 HIS B 409 ASN B 413 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5172 Z= 0.233 Angle : 0.725 20.014 7034 Z= 0.350 Chirality : 0.042 0.141 838 Planarity : 0.006 0.054 878 Dihedral : 7.243 29.655 686 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 0.91 % Allowed : 8.15 % Favored : 90.94 % 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: -5.54 (0.26), residues: 642 helix: -4.25 (0.16), residues: 354 sheet: -1.36 (0.80), residues: 46 loop : -2.89 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 375 HIS 0.003 0.001 HIS B 373 PHE 0.012 0.001 PHE B 94 TYR 0.016 0.002 TYR B 270 ARG 0.002 0.001 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8164 (ttp-170) cc_final: 0.7945 (ttm-80) REVERT: A 78 GLU cc_start: 0.7964 (pt0) cc_final: 0.7658 (pt0) REVERT: A 99 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7348 (tm-30) REVERT: B 44 MET cc_start: 0.7732 (mtm) cc_final: 0.7521 (mtt) REVERT: B 78 GLU cc_start: 0.7841 (pt0) cc_final: 0.7559 (pt0) REVERT: B 80 MET cc_start: 0.8790 (ptm) cc_final: 0.8347 (ptm) REVERT: B 99 GLU cc_start: 0.7429 (tm-30) cc_final: 0.7117 (tm-30) REVERT: B 371 GLU cc_start: 0.8092 (tp30) cc_final: 0.7848 (tp30) outliers start: 5 outliers final: 3 residues processed: 88 average time/residue: 0.1356 time to fit residues: 16.4150 Evaluate side-chains 74 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 125 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 255 ASN B 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5172 Z= 0.176 Angle : 0.659 19.139 7034 Z= 0.315 Chirality : 0.041 0.143 838 Planarity : 0.004 0.036 878 Dihedral : 6.464 28.013 686 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 0.91 % Allowed : 11.41 % Favored : 87.68 % 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: -4.76 (0.29), residues: 642 helix: -3.55 (0.21), residues: 354 sheet: -0.94 (0.80), residues: 46 loop : -2.67 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 375 HIS 0.002 0.001 HIS A 373 PHE 0.010 0.001 PHE A 94 TYR 0.023 0.002 TYR B 270 ARG 0.002 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7250 (mm-30) REVERT: A 99 GLU cc_start: 0.7448 (tm-30) cc_final: 0.7212 (tm-30) REVERT: B 58 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7435 (mm-30) REVERT: B 80 MET cc_start: 0.8713 (ptm) cc_final: 0.8433 (ptm) REVERT: B 371 GLU cc_start: 0.8015 (tp30) cc_final: 0.7791 (tp30) outliers start: 5 outliers final: 3 residues processed: 79 average time/residue: 0.1536 time to fit residues: 16.3852 Evaluate side-chains 74 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 125 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.8006 > 50: distance: 49 - 53: 22.867 distance: 53 - 54: 11.155 distance: 54 - 55: 16.038 distance: 54 - 57: 39.018 distance: 55 - 56: 44.907 distance: 55 - 64: 44.173 distance: 57 - 58: 11.958 distance: 58 - 59: 13.069 distance: 58 - 60: 14.681 distance: 59 - 61: 21.798 distance: 60 - 62: 17.508 distance: 61 - 63: 9.240 distance: 62 - 63: 6.653 distance: 64 - 65: 29.448 distance: 64 - 70: 33.138 distance: 65 - 66: 41.076 distance: 65 - 68: 32.176 distance: 66 - 67: 28.915 distance: 66 - 71: 36.279 distance: 68 - 69: 14.815 distance: 69 - 70: 12.084 distance: 71 - 72: 9.105 distance: 72 - 73: 10.671 distance: 72 - 75: 8.280 distance: 73 - 74: 34.590 distance: 73 - 79: 14.546 distance: 75 - 76: 6.941 distance: 76 - 77: 13.828 distance: 76 - 78: 6.560 distance: 79 - 80: 9.956 distance: 79 - 85: 17.924 distance: 80 - 81: 24.268 distance: 80 - 83: 14.158 distance: 81 - 82: 41.182 distance: 83 - 84: 16.512 distance: 84 - 85: 24.336 distance: 86 - 87: 37.871 distance: 87 - 88: 19.236 distance: 87 - 90: 6.890 distance: 88 - 89: 41.985 distance: 88 - 92: 24.614 distance: 90 - 91: 22.630 distance: 92 - 93: 31.671 distance: 93 - 94: 21.082 distance: 93 - 96: 16.648 distance: 94 - 95: 20.896 distance: 94 - 101: 21.547 distance: 96 - 97: 11.581 distance: 97 - 98: 29.056 distance: 98 - 99: 10.311 distance: 101 - 102: 8.192 distance: 102 - 103: 41.405 distance: 102 - 105: 52.703 distance: 103 - 104: 49.110 distance: 103 - 106: 31.289 distance: 106 - 107: 13.998 distance: 107 - 108: 10.544 distance: 107 - 110: 48.003 distance: 108 - 109: 24.054 distance: 108 - 117: 7.219 distance: 110 - 111: 16.787 distance: 111 - 112: 14.002 distance: 111 - 113: 16.954 distance: 112 - 114: 8.541 distance: 113 - 115: 11.930 distance: 115 - 116: 5.297 distance: 117 - 118: 14.851 distance: 118 - 119: 32.293 distance: 118 - 121: 29.313 distance: 119 - 120: 28.304 distance: 119 - 124: 16.857 distance: 121 - 122: 11.101 distance: 121 - 123: 19.313 distance: 124 - 125: 11.421 distance: 125 - 126: 23.381 distance: 125 - 128: 32.060 distance: 126 - 127: 21.554 distance: 126 - 133: 8.658 distance: 128 - 129: 14.803 distance: 129 - 130: 14.616 distance: 130 - 131: 6.112 distance: 130 - 132: 5.407