Starting phenix.real_space_refine on Fri Aug 2 23:52:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woz_37703/08_2024/8woz_37703.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woz_37703/08_2024/8woz_37703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woz_37703/08_2024/8woz_37703.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woz_37703/08_2024/8woz_37703.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woz_37703/08_2024/8woz_37703.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8woz_37703/08_2024/8woz_37703.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 36 5.16 5 C 3994 2.51 5 N 1032 2.21 5 O 1181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 38": "OD1" <-> "OD2" Residue "A ASP 49": "OD1" <-> "OD2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 295": "OD1" <-> "OD2" Residue "A PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 499": "OD1" <-> "OD2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A GLU 597": "OE1" <-> "OE2" Residue "B TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 6244 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4858 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 26, 'TRANS': 569} Chain: "B" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1385 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 160} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.13, per 1000 atoms: 0.66 Number of scatterers: 6244 At special positions: 0 Unit cell: (77.28, 97.98, 107.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 36 16.00 O 1181 8.00 N 1032 7.00 C 3994 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " 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: 2.24 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 374 " 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1450 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 4 sheets defined 54.9% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.876A pdb=" N LEU A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 78 removed outlier: 3.612A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 removed outlier: 4.224A pdb=" N THR A 82 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.868A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.783A pdb=" N ALA A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.712A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.841A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 221 through 247 removed outlier: 3.516A pdb=" N GLU A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.659A pdb=" N PHE A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 removed outlier: 4.059A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.841A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.762A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 405 removed outlier: 3.927A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 413 removed outlier: 4.188A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.778A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 removed outlier: 3.512A pdb=" N THR A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A 466 " --> pdb=" O MET A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.679A pdb=" N LYS A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.832A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.524A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 4.613A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.606A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 352 through 356 removed outlier: 3.616A pdb=" N LEU B 355 " --> pdb=" O TYR B 352 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR B 356 " --> pdb=" O SER B 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 356' Processing helix chain 'B' and resid 372 through 377 removed outlier: 4.358A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 377 " --> pdb=" O LEU B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 397 removed outlier: 4.323A pdb=" N ARG B 395 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.610A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.143A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 341 through 345 Processing sheet with id=AA4, first strand: chain 'B' and resid 439 through 441 276 hydrogen bonds defined for protein. 774 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: 1.47 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1261 1.33 - 1.45: 1667 1.45 - 1.57: 3434 1.57 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 6420 Sorted by residual: bond pdb=" N ASP A 292 " pdb=" CA ASP A 292 " ideal model delta sigma weight residual 1.457 1.502 -0.045 1.29e-02 6.01e+03 1.19e+01 bond pdb=" N HIS A 378 " pdb=" CA HIS A 378 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.21e-02 6.83e+03 8.43e+00 bond pdb=" N ASN A 90 " pdb=" CA ASN A 90 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.31e-02 5.83e+03 6.78e+00 bond pdb=" N VAL A 293 " pdb=" CA VAL A 293 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.25e-02 6.40e+03 6.38e+00 bond pdb=" C ASP A 292 " pdb=" O ASP A 292 " ideal model delta sigma weight residual 1.235 1.208 0.028 1.26e-02 6.30e+03 4.78e+00 ... (remaining 6415 not shown) Histogram of bond angle deviations from ideal: 96.66 - 104.13: 101 104.13 - 111.61: 2725 111.61 - 119.08: 2376 119.08 - 126.56: 3382 126.56 - 134.03: 140 Bond angle restraints: 8724 Sorted by residual: angle pdb=" CA HIS A 378 " pdb=" CB HIS A 378 " pdb=" CG HIS A 378 " ideal model delta sigma weight residual 113.80 119.10 -5.30 1.00e+00 1.00e+00 2.81e+01 angle pdb=" C ASP A 292 " pdb=" CA ASP A 292 " pdb=" CB ASP A 292 " ideal model delta sigma weight residual 110.42 99.96 10.46 1.99e+00 2.53e-01 2.76e+01 angle pdb=" C HIS A 378 " pdb=" CA HIS A 378 " pdb=" CB HIS A 378 " ideal model delta sigma weight residual 110.79 102.59 8.20 1.66e+00 3.63e-01 2.44e+01 angle pdb=" O GLY A 377 " pdb=" C GLY A 377 " pdb=" N HIS A 378 " ideal model delta sigma weight residual 122.19 117.62 4.57 9.60e-01 1.09e+00 2.27e+01 angle pdb=" CA GLY A 377 " pdb=" C GLY A 377 " pdb=" N HIS A 378 " ideal model delta sigma weight residual 117.04 121.49 -4.45 9.90e-01 1.02e+00 2.02e+01 ... (remaining 8719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 3262 17.74 - 35.49: 398 35.49 - 53.23: 113 53.23 - 70.97: 9 70.97 - 88.71: 8 Dihedral angle restraints: 3790 sinusoidal: 1530 harmonic: 2260 Sorted by residual: dihedral pdb=" CB CYS A 344 " pdb=" SG CYS A 344 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -126.19 40.19 1 1.00e+01 1.00e-02 2.27e+01 dihedral pdb=" CA TRP A 473 " pdb=" C TRP A 473 " pdb=" N MET A 474 " pdb=" CA MET A 474 " ideal model delta harmonic sigma weight residual 180.00 -160.85 -19.15 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CB CYS B 467 " pdb=" SG CYS B 467 " pdb=" SG CYS B 474 " pdb=" CB CYS B 474 " ideal model delta sinusoidal sigma weight residual -86.00 -55.24 -30.76 1 1.00e+01 1.00e-02 1.35e+01 ... (remaining 3787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 578 0.035 - 0.071: 246 0.071 - 0.106: 65 0.106 - 0.141: 18 0.141 - 0.176: 3 Chirality restraints: 910 Sorted by residual: chirality pdb=" CG LEU A 267 " pdb=" CB LEU A 267 " pdb=" CD1 LEU A 267 " pdb=" CD2 LEU A 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" CB VAL A 581 " pdb=" CA VAL A 581 " pdb=" CG1 VAL A 581 " pdb=" CG2 VAL A 581 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA HIS A 378 " pdb=" N HIS A 378 " pdb=" C HIS A 378 " pdb=" CB HIS A 378 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 907 not shown) Planarity restraints: 1127 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 257 " -0.072 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO A 258 " 0.186 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 398 " 0.045 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRO B 399 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 399 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 399 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 378 " -0.025 2.00e-02 2.50e+03 2.04e-02 6.24e+00 pdb=" CG HIS A 378 " 0.040 2.00e-02 2.50e+03 pdb=" ND1 HIS A 378 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS A 378 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS A 378 " -0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS A 378 " -0.015 2.00e-02 2.50e+03 ... (remaining 1124 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 143 2.70 - 3.25: 6140 3.25 - 3.80: 9376 3.80 - 4.35: 11814 4.35 - 4.90: 19566 Nonbonded interactions: 47039 Sorted by model distance: nonbonded pdb=" O VAL A 293 " pdb=" OG1 THR A 294 " model vdw 2.147 3.040 nonbonded pdb=" NH1 ARG A 177 " pdb=" O GLU A 495 " model vdw 2.241 3.120 nonbonded pdb=" OG SER B 362 " pdb=" O ALA B 422 " model vdw 2.243 3.040 nonbonded pdb=" ND2 ASN A 137 " pdb=" OE1 GLN A 139 " model vdw 2.249 3.120 nonbonded pdb=" OD1 ASP A 198 " pdb=" N ASP A 201 " model vdw 2.314 3.120 ... (remaining 47034 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.200 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 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 : 0.003 0.052 6420 Z= 0.215 Angle : 0.704 12.263 8724 Z= 0.395 Chirality : 0.042 0.176 910 Planarity : 0.006 0.107 1127 Dihedral : 16.315 88.714 2328 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.15 % Allowed : 22.88 % Favored : 76.97 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 2.70 % 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: -0.58 (0.32), residues: 764 helix: 0.44 (0.28), residues: 381 sheet: 0.84 (0.81), residues: 40 loop : -1.48 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 594 HIS 0.012 0.001 HIS A 378 PHE 0.018 0.001 PHE A 72 TYR 0.015 0.001 TYR A 183 ARG 0.002 0.000 ARG A 245 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 0.620 Fit side-chains REVERT: A 207 TYR cc_start: 0.7010 (m-10) cc_final: 0.6729 (m-10) REVERT: A 247 LYS cc_start: 0.6663 (tptt) cc_final: 0.6414 (mmtt) REVERT: A 539 LEU cc_start: 0.8697 (tp) cc_final: 0.8487 (tt) outliers start: 1 outliers final: 1 residues processed: 118 average time/residue: 0.1714 time to fit residues: 27.1282 Evaluate side-chains 114 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 31 optimal weight: 0.0020 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 59 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 36 optimal weight: 0.2980 chunk 44 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6420 Z= 0.191 Angle : 0.582 11.438 8724 Z= 0.300 Chirality : 0.041 0.159 910 Planarity : 0.005 0.074 1127 Dihedral : 4.678 56.899 843 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.08 % Allowed : 20.80 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.40 (0.31), residues: 764 helix: 0.65 (0.27), residues: 389 sheet: 0.87 (0.80), residues: 42 loop : -1.53 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.004 0.001 HIS A 241 PHE 0.016 0.001 PHE A 603 TYR 0.014 0.001 TYR A 183 ARG 0.004 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 0.652 Fit side-chains REVERT: A 471 GLU cc_start: 0.7703 (pm20) cc_final: 0.7402 (pm20) REVERT: A 539 LEU cc_start: 0.8710 (tp) cc_final: 0.8483 (tt) outliers start: 14 outliers final: 5 residues processed: 127 average time/residue: 0.1599 time to fit residues: 27.7150 Evaluate side-chains 115 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 110 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain B residue 337 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 46 optimal weight: 0.4980 chunk 19 optimal weight: 0.0020 chunk 69 optimal weight: 0.4980 chunk 74 optimal weight: 0.3980 chunk 61 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 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 0.044 6420 Z= 0.179 Angle : 0.567 11.253 8724 Z= 0.292 Chirality : 0.040 0.143 910 Planarity : 0.005 0.063 1127 Dihedral : 4.113 15.565 841 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.38 % Allowed : 20.51 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.23 (0.31), residues: 764 helix: 0.81 (0.27), residues: 388 sheet: 1.03 (0.81), residues: 42 loop : -1.49 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.004 0.001 HIS A 241 PHE 0.016 0.001 PHE A 603 TYR 0.015 0.001 TYR A 183 ARG 0.002 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 0.506 Fit side-chains REVERT: A 190 MET cc_start: 0.7598 (tmm) cc_final: 0.7174 (tmm) REVERT: A 364 VAL cc_start: 0.6590 (OUTLIER) cc_final: 0.6249 (t) REVERT: A 471 GLU cc_start: 0.7717 (pm20) cc_final: 0.7399 (pm20) REVERT: A 594 TRP cc_start: 0.7172 (OUTLIER) cc_final: 0.6865 (t-100) REVERT: A 596 LYS cc_start: 0.8375 (mtpt) cc_final: 0.8072 (mttp) outliers start: 16 outliers final: 9 residues processed: 124 average time/residue: 0.1545 time to fit residues: 25.7508 Evaluate side-chains 122 residues out of total 673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 594 TRP Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 355 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: 68.6599 > 50: distance: 78 - 82: 27.275 distance: 81 - 129: 24.795 distance: 82 - 83: 34.352 distance: 83 - 84: 30.524 distance: 83 - 86: 41.035 distance: 86 - 87: 27.528 distance: 86 - 88: 16.267 distance: 89 - 95: 39.596 distance: 90 - 91: 5.781 distance: 91 - 92: 34.456 distance: 91 - 96: 23.205 distance: 94 - 95: 39.659 distance: 96 - 97: 49.271 distance: 96 - 102: 14.383 distance: 97 - 98: 10.292 distance: 97 - 100: 42.316 distance: 98 - 99: 27.206 distance: 98 - 103: 37.279 distance: 100 - 101: 28.343 distance: 101 - 102: 40.286 distance: 103 - 104: 3.337 distance: 104 - 105: 43.986 distance: 104 - 107: 29.304 distance: 105 - 106: 35.935 distance: 105 - 108: 20.462 distance: 108 - 109: 8.073 distance: 109 - 110: 38.577 distance: 109 - 112: 10.487 distance: 110 - 111: 14.357 distance: 110 - 116: 46.601 distance: 112 - 113: 52.961 distance: 113 - 114: 26.877 distance: 113 - 115: 34.958 distance: 116 - 117: 13.037 distance: 117 - 118: 22.980 distance: 117 - 120: 17.730 distance: 118 - 119: 22.836 distance: 118 - 124: 40.309 distance: 120 - 121: 5.606 distance: 121 - 122: 27.377 distance: 121 - 123: 47.876 distance: 124 - 125: 12.124 distance: 125 - 126: 12.823 distance: 125 - 128: 37.644 distance: 126 - 127: 5.690 distance: 126 - 130: 5.070 distance: 128 - 129: 31.589 distance: 130 - 131: 21.288 distance: 131 - 132: 27.368 distance: 131 - 134: 56.334 distance: 132 - 133: 12.413 distance: 132 - 142: 27.241 distance: 134 - 135: 9.269 distance: 135 - 136: 8.035 distance: 135 - 137: 14.891 distance: 136 - 138: 16.047 distance: 137 - 139: 17.962 distance: 138 - 140: 11.835 distance: 139 - 140: 16.780 distance: 142 - 143: 21.900 distance: 143 - 144: 19.500 distance: 143 - 146: 33.195 distance: 144 - 156: 37.163 distance: 146 - 147: 16.198 distance: 147 - 148: 18.650 distance: 147 - 149: 15.428 distance: 149 - 151: 6.192 distance: 149 - 152: 8.204 distance: 151 - 153: 13.667 distance: 152 - 154: 8.531 distance: 153 - 155: 6.368 distance: 154 - 155: 11.610 distance: 156 - 162: 15.318 distance: 157 - 160: 22.403 distance: 158 - 159: 12.544 distance: 158 - 163: 34.473 distance: 160 - 161: 23.947 distance: 161 - 162: 16.530