Starting phenix.real_space_refine on Thu May 15 06:29:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sd0_25044/05_2025/7sd0_25044.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sd0_25044/05_2025/7sd0_25044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sd0_25044/05_2025/7sd0_25044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sd0_25044/05_2025/7sd0_25044.map" model { file = "/net/cci-nas-00/data/ceres_data/7sd0_25044/05_2025/7sd0_25044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sd0_25044/05_2025/7sd0_25044.cif" } resolution = 2.95 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6177 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Mn 2 7.51 5 P 3 5.49 5 Mg 1 5.21 5 S 40 5.16 5 C 4911 2.51 5 N 1316 2.21 5 O 1456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7729 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3930 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 25, 'TRANS': 473} Chain breaks: 1 Chain: "B" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1407 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 165} Chain: "C" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2357 Classifications: {'peptide': 292} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 278} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.98, per 1000 atoms: 0.64 Number of scatterers: 7729 At special positions: 0 Unit cell: (89.666, 85.476, 104.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 2 24.99 S 40 16.00 P 3 15.00 Mg 1 11.99 O 1456 8.00 N 1316 7.00 C 4911 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 929.7 milliseconds 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 35.1% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 116 through 122 Processing helix chain 'A' and resid 141 through 145 Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 187 through 191 removed outlier: 3.539A pdb=" N LEU A 191 " --> pdb=" O VAL A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 237 removed outlier: 3.709A pdb=" N GLY A 235 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 260 removed outlier: 3.547A pdb=" N ILE A 257 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY A 258 " --> pdb=" O LYS A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.736A pdb=" N GLY A 281 " --> pdb=" O ASP A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 306 Processing helix chain 'A' and resid 324 through 329 removed outlier: 3.972A pdb=" N SER A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.539A pdb=" N PHE A 354 " --> pdb=" O PRO A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 401 removed outlier: 4.368A pdb=" N GLY A 399 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP A 401 " --> pdb=" O PHE A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 424 removed outlier: 3.511A pdb=" N VAL A 421 " --> pdb=" O PRO A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 447 removed outlier: 3.553A pdb=" N GLY A 445 " --> pdb=" O HIS A 442 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 447 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 469 removed outlier: 3.593A pdb=" N ILE A 467 " --> pdb=" O PRO A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 516 removed outlier: 3.834A pdb=" N ILE A 513 " --> pdb=" O PRO A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 540 Processing helix chain 'A' and resid 557 through 564 removed outlier: 3.737A pdb=" N GLY A 564 " --> pdb=" O ILE A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 574 Processing helix chain 'B' and resid 25 through 36 Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 77 through 84 removed outlier: 3.754A pdb=" N THR B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 115 removed outlier: 3.958A pdb=" N PHE B 100 " --> pdb=" O ASP B 96 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASP B 104 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG B 105 " --> pdb=" O GLU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 134 Processing helix chain 'B' and resid 137 through 148 Processing helix chain 'B' and resid 163 through 178 removed outlier: 3.693A pdb=" N PHE B 168 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN B 178 " --> pdb=" O VAL B 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 18 Processing helix chain 'C' and resid 31 through 49 removed outlier: 3.805A pdb=" N ILE C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU C 44 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE C 45 " --> pdb=" O LYS C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 80 removed outlier: 3.585A pdb=" N LEU C 73 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG C 74 " --> pdb=" O TYR C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 114 removed outlier: 3.549A pdb=" N ILE C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 127 removed outlier: 3.501A pdb=" N CYS C 127 " --> pdb=" O ASN C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 134 removed outlier: 3.876A pdb=" N ILE C 133 " --> pdb=" O SER C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 144 removed outlier: 3.549A pdb=" N LYS C 141 " --> pdb=" O TYR C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 157 removed outlier: 3.651A pdb=" N LYS C 150 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 188 removed outlier: 4.261A pdb=" N ILE C 186 " --> pdb=" O SER C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 207 removed outlier: 3.805A pdb=" N ASP C 203 " --> pdb=" O GLY C 199 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 240 removed outlier: 3.806A pdb=" N VAL C 232 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA C 233 " --> pdb=" O ALA C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 275 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 66 removed outlier: 6.757A pdb=" N ALA A 65 " --> pdb=" O CYS C 291 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N PHE C 293 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LYS C 60 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 106 removed outlier: 6.788A pdb=" N LEU A 105 " --> pdb=" O TYR A 129 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU A 289 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ASN A 313 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU A 312 " --> pdb=" O THR A 337 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN A 361 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 429 through 431 removed outlier: 3.612A pdb=" N ASP A 454 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU A 453 " --> pdb=" O VAL A 477 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 499 " --> pdb=" O GLU A 521 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR A 523 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU A 522 " --> pdb=" O SER A 547 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 48 through 49 Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 49 removed outlier: 6.116A pdb=" N TYR B 14 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU B 66 " --> pdb=" O TYR B 14 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU B 16 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE B 88 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL B 124 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE B 90 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ASN B 126 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N TYR B 92 " --> pdb=" O ASN B 126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 52 through 55 removed outlier: 6.001A pdb=" N LEU C 53 " --> pdb=" O ILE C 164 " (cutoff:3.500A) 222 hydrogen bonds defined for protein. 510 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.08 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1309 1.30 - 1.43: 1865 1.43 - 1.56: 4627 1.56 - 1.69: 7 1.69 - 1.82: 61 Bond restraints: 7869 Sorted by residual: bond pdb=" CA ASP C 92 " pdb=" C ASP C 92 " ideal model delta sigma weight residual 1.532 1.462 0.070 9.60e-03 1.09e+04 5.33e+01 bond pdb=" C ASP C 208 " pdb=" O ASP C 208 " ideal model delta sigma weight residual 1.240 1.170 0.070 1.24e-02 6.50e+03 3.21e+01 bond pdb=" CA HIS C 125 " pdb=" C HIS C 125 " ideal model delta sigma weight residual 1.524 1.437 0.087 1.66e-02 3.63e+03 2.74e+01 bond pdb=" CA GLN C 262 " pdb=" C GLN C 262 " ideal model delta sigma weight residual 1.522 1.452 0.070 1.40e-02 5.10e+03 2.50e+01 bond pdb=" N GLN C 262 " pdb=" CA GLN C 262 " ideal model delta sigma weight residual 1.458 1.392 0.066 1.33e-02 5.65e+03 2.45e+01 ... (remaining 7864 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 10262 2.29 - 4.58: 317 4.58 - 6.87: 49 6.87 - 9.16: 23 9.16 - 11.45: 6 Bond angle restraints: 10657 Sorted by residual: angle pdb=" N SER C 268 " pdb=" CA SER C 268 " pdb=" C SER C 268 " ideal model delta sigma weight residual 112.59 121.87 -9.28 1.22e+00 6.72e-01 5.79e+01 angle pdb=" N HIS C 173 " pdb=" CA HIS C 173 " pdb=" C HIS C 173 " ideal model delta sigma weight residual 111.07 118.65 -7.58 1.07e+00 8.73e-01 5.02e+01 angle pdb=" N TYR C 69 " pdb=" CA TYR C 69 " pdb=" C TYR C 69 " ideal model delta sigma weight residual 112.38 120.62 -8.24 1.22e+00 6.72e-01 4.56e+01 angle pdb=" C ALA C 269 " pdb=" N PRO C 270 " pdb=" CA PRO C 270 " ideal model delta sigma weight residual 120.21 114.20 6.01 9.60e-01 1.09e+00 3.93e+01 angle pdb=" N TYR C 272 " pdb=" CA TYR C 272 " pdb=" C TYR C 272 " ideal model delta sigma weight residual 110.30 119.49 -9.19 1.50e+00 4.44e-01 3.76e+01 ... (remaining 10652 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 4345 16.69 - 33.37: 392 33.37 - 50.06: 91 50.06 - 66.74: 13 66.74 - 83.43: 7 Dihedral angle restraints: 4848 sinusoidal: 2029 harmonic: 2819 Sorted by residual: dihedral pdb=" N ASP C 64 " pdb=" C ASP C 64 " pdb=" CA ASP C 64 " pdb=" CB ASP C 64 " ideal model delta harmonic sigma weight residual 122.80 133.86 -11.06 0 2.50e+00 1.60e-01 1.96e+01 dihedral pdb=" C ARG C 246 " pdb=" N ARG C 246 " pdb=" CA ARG C 246 " pdb=" CB ARG C 246 " ideal model delta harmonic sigma weight residual -122.60 -133.30 10.70 0 2.50e+00 1.60e-01 1.83e+01 dihedral pdb=" C ARG C 96 " pdb=" N ARG C 96 " pdb=" CA ARG C 96 " pdb=" CB ARG C 96 " ideal model delta harmonic sigma weight residual -122.60 -132.33 9.73 0 2.50e+00 1.60e-01 1.52e+01 ... (remaining 4845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1104 0.091 - 0.181: 89 0.181 - 0.272: 16 0.272 - 0.363: 11 0.363 - 0.454: 8 Chirality restraints: 1228 Sorted by residual: chirality pdb=" CA ASP C 64 " pdb=" N ASP C 64 " pdb=" C ASP C 64 " pdb=" CB ASP C 64 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" CA ARG C 246 " pdb=" N ARG C 246 " pdb=" C ARG C 246 " pdb=" CB ARG C 246 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" CA ARG C 261 " pdb=" N ARG C 261 " pdb=" C ARG C 261 " pdb=" CB ARG C 261 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.29e+00 ... (remaining 1225 not shown) Planarity restraints: 1366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 295 " -0.020 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C ILE C 295 " 0.068 2.00e-02 2.50e+03 pdb=" O ILE C 295 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU C 296 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 90 " 0.018 2.00e-02 2.50e+03 3.43e-02 1.17e+01 pdb=" C LEU C 90 " -0.059 2.00e-02 2.50e+03 pdb=" O LEU C 90 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY C 91 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 89 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.96e+00 pdb=" C PHE C 89 " -0.049 2.00e-02 2.50e+03 pdb=" O PHE C 89 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU C 90 " 0.016 2.00e-02 2.50e+03 ... (remaining 1363 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 26 2.43 - 3.05: 4865 3.05 - 3.67: 11840 3.67 - 4.28: 17782 4.28 - 4.90: 29613 Nonbonded interactions: 64126 Sorted by model distance: nonbonded pdb=" OD1 ASN C 124 " pdb="MN MN C 400 " model vdw 1.813 2.320 nonbonded pdb=" OG1 THR B 45 " pdb="MG MG B 501 " model vdw 1.848 2.170 nonbonded pdb=" O GLN A 474 " pdb=" OG1 THR A 497 " model vdw 2.229 3.040 nonbonded pdb=" O THR A 494 " pdb=" ND2 ASN A 518 " model vdw 2.232 3.120 nonbonded pdb=" O GLY C 80 " pdb=" OH TYR C 87 " model vdw 2.243 3.040 ... (remaining 64121 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.630 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 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 : 0.007 0.099 7869 Z= 0.469 Angle : 0.972 11.454 10657 Z= 0.579 Chirality : 0.069 0.454 1228 Planarity : 0.005 0.049 1366 Dihedral : 13.551 83.428 3018 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.91 % Allowed : 2.28 % Favored : 96.81 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 8.70 % 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: -2.03 (0.27), residues: 957 helix: -1.87 (0.27), residues: 289 sheet: -1.57 (0.48), residues: 138 loop : -0.86 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 206 HIS 0.012 0.002 HIS C 248 PHE 0.011 0.001 PHE C 257 TYR 0.012 0.002 TYR C 93 ARG 0.003 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.29094 ( 220) hydrogen bonds : angle 8.61469 ( 510) covalent geometry : bond 0.00698 ( 7869) covalent geometry : angle 0.97188 (10657) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: A 446 ASN cc_start: 0.7828 (m110) cc_final: 0.7468 (m110) REVERT: C 31 GLN cc_start: 0.7339 (mt0) cc_final: 0.6813 (tm-30) REVERT: C 32 GLU cc_start: 0.7889 (pm20) cc_final: 0.7668 (pm20) REVERT: C 219 ASN cc_start: 0.7288 (m110) cc_final: 0.6951 (m110) outliers start: 8 outliers final: 3 residues processed: 129 average time/residue: 1.1375 time to fit residues: 156.1429 Evaluate side-chains 80 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 295 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 0.0980 chunk 48 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 45 optimal weight: 0.0670 chunk 55 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 498 HIS B 58 ASN B 148 HIS C 125 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.116212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.092139 restraints weight = 16568.975| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 3.73 r_work: 0.3552 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7869 Z= 0.125 Angle : 0.631 8.620 10657 Z= 0.324 Chirality : 0.043 0.154 1228 Planarity : 0.004 0.041 1366 Dihedral : 5.666 75.994 1072 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.48 % Allowed : 11.05 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.27), residues: 957 helix: -1.05 (0.29), residues: 300 sheet: -1.48 (0.39), residues: 180 loop : -0.74 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 206 HIS 0.008 0.001 HIS C 173 PHE 0.026 0.001 PHE A 571 TYR 0.022 0.001 TYR A 469 ARG 0.004 0.000 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.04859 ( 220) hydrogen bonds : angle 5.54255 ( 510) covalent geometry : bond 0.00281 ( 7869) covalent geometry : angle 0.63123 (10657) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1914 Ramachandran restraints generated. 957 Oldfield, 0 Emsley, 957 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 ASP cc_start: 0.7531 (t0) cc_final: 0.7299 (m-30) REVERT: A 446 ASN cc_start: 0.7690 (m110) cc_final: 0.7288 (m110) REVERT: B 59 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7550 (mm-40) REVERT: B 96 ASP cc_start: 0.7457 (t70) cc_final: 0.7219 (p0) REVERT: C 32 GLU cc_start: 0.8339 (pm20) cc_final: 0.8083 (pm20) REVERT: C 183 MET cc_start: 0.7968 (mpp) cc_final: 0.7689 (mpp) REVERT: C 283 MET cc_start: 0.8221 (ttm) cc_final: 0.7997 (ttm) outliers start: 13 outliers final: 3 residues processed: 104 average time/residue: 1.0573 time to fit residues: 117.5888 Evaluate side-chains 76 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain C residue 213 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.7618 > 50: distance: 42 - 46: 16.159 distance: 46 - 47: 26.889 distance: 47 - 48: 42.913 distance: 47 - 50: 32.700 distance: 48 - 49: 22.829 distance: 48 - 54: 32.805 distance: 50 - 51: 44.473 distance: 54 - 55: 26.043 distance: 55 - 56: 32.457 distance: 55 - 58: 31.487 distance: 56 - 57: 39.470 distance: 56 - 64: 10.749 distance: 58 - 59: 38.940 distance: 59 - 60: 44.002 distance: 59 - 61: 38.238 distance: 60 - 62: 48.502 distance: 62 - 63: 11.002 distance: 64 - 65: 8.358 distance: 65 - 66: 9.564 distance: 66 - 67: 24.237 distance: 66 - 70: 24.490 distance: 68 - 69: 26.617 distance: 70 - 71: 43.193 distance: 71 - 72: 40.616 distance: 72 - 78: 13.701 distance: 74 - 75: 24.855 distance: 75 - 76: 39.510 distance: 75 - 77: 41.975 distance: 78 - 79: 4.787 distance: 78 - 84: 42.739 distance: 79 - 80: 10.596 distance: 80 - 81: 40.644 distance: 80 - 85: 16.792 distance: 82 - 83: 42.094 distance: 85 - 86: 18.723 distance: 86 - 87: 30.391 distance: 86 - 89: 14.908 distance: 87 - 88: 42.052 distance: 87 - 96: 12.484 distance: 88 - 113: 43.681 distance: 89 - 90: 27.212 distance: 90 - 91: 9.396 distance: 90 - 92: 28.453 distance: 91 - 93: 11.494 distance: 92 - 94: 21.991 distance: 93 - 95: 12.334 distance: 94 - 95: 6.154 distance: 97 - 100: 30.715 distance: 98 - 99: 14.540 distance: 99 - 118: 13.086 distance: 100 - 101: 15.051 distance: 101 - 102: 18.487 distance: 102 - 103: 14.783 distance: 102 - 104: 13.809 distance: 106 - 107: 12.162 distance: 106 - 109: 11.039 distance: 107 - 108: 12.053 distance: 107 - 113: 9.448 distance: 108 - 126: 27.416 distance: 109 - 110: 22.355 distance: 110 - 111: 26.353 distance: 110 - 112: 31.713 distance: 113 - 114: 24.721 distance: 114 - 115: 6.043 distance: 114 - 117: 32.994 distance: 115 - 116: 9.828 distance: 115 - 118: 36.210 distance: 118 - 119: 60.526 distance: 119 - 120: 6.889 distance: 119 - 122: 9.802 distance: 120 - 121: 6.241 distance: 120 - 126: 30.978 distance: 122 - 123: 17.794 distance: 123 - 124: 21.335 distance: 123 - 125: 12.711