Starting phenix.real_space_refine on Sat Jan 20 06:11:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsf_32756/01_2024/7wsf_32756.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsf_32756/01_2024/7wsf_32756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsf_32756/01_2024/7wsf_32756.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsf_32756/01_2024/7wsf_32756.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsf_32756/01_2024/7wsf_32756.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsf_32756/01_2024/7wsf_32756.pdb" } resolution = 2.87 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= 0.053 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 6717 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 38 5.16 5 C 4590 2.51 5 N 1192 2.21 5 O 1349 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 7170 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5677 Classifications: {'peptide': 693} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 659} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 16 Chain: "B" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1492 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 173} 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: 4.73, per 1000 atoms: 0.66 Number of scatterers: 7170 At special positions: 0 Unit cell: (72.252, 94.998, 140.49, 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 38 16.00 O 1349 8.00 N 1192 7.00 C 4590 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 529 " - pdb=" SG CYS A 541 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " 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: 2.88 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 373 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 377 " 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 7 sheets defined 55.2% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 Processing helix chain 'A' and resid 56 through 81 removed outlier: 3.614A pdb=" N GLN A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.667A pdb=" N SER A 106 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.700A pdb=" N ASN A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 153 removed outlier: 3.600A pdb=" N ILE A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 193 removed outlier: 4.091A pdb=" N LYS A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Proline residue: A 177 - end of helix Processing helix chain 'A' and resid 197 through 203 Processing helix chain 'A' and resid 204 through 207 Processing helix chain 'A' and resid 217 through 251 removed outlier: 3.877A pdb=" N ILE A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) Proline residue: A 234 - end of helix Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 292 through 298 removed outlier: 3.546A pdb=" N ASN A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 317 removed outlier: 3.554A pdb=" N PHE A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 330 removed outlier: 3.703A pdb=" N TRP A 327 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 328 " --> pdb=" O GLN A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 384 removed outlier: 3.618A pdb=" N HIS A 372 " --> pdb=" O PHE A 368 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 388 through 392 Processing helix chain 'A' and resid 398 through 412 removed outlier: 3.625A pdb=" N GLY A 404 " --> pdb=" O HIS A 400 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 420 Processing helix chain 'A' and resid 430 through 446 removed outlier: 3.640A pdb=" N GLN A 444 " --> pdb=" O LYS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 471 through 481 Processing helix chain 'A' and resid 498 through 501 Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 512 through 532 removed outlier: 3.872A pdb=" N THR A 518 " --> pdb=" O TYR A 514 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 removed outlier: 3.519A pdb=" N CYS A 541 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 558 removed outlier: 3.576A pdb=" N GLY A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N MET A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 574 removed outlier: 3.739A pdb=" N ILE A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 587 removed outlier: 3.589A pdb=" N PHE A 587 " --> pdb=" O LEU A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 598 Processing helix chain 'A' and resid 638 through 657 removed outlier: 4.259A pdb=" N PHE A 642 " --> pdb=" O GLU A 638 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN A 643 " --> pdb=" O MET A 639 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 647 " --> pdb=" O GLN A 643 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TYR A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 706 removed outlier: 3.596A pdb=" N SER A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 352 through 358 removed outlier: 3.890A pdb=" N TYR B 356 " --> pdb=" O TYR B 352 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER B 358 " --> pdb=" O VAL B 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 358' Processing helix chain 'B' and resid 371 through 375 removed outlier: 4.012A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 397 Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 425 through 430 Processing helix chain 'B' and resid 488 through 492 removed outlier: 3.501A pdb=" N GLN B 492 " --> pdb=" O ILE B 489 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 261 through 262 removed outlier: 5.840A pdb=" N LEU A 261 " --> pdb=" O VAL A 487 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 351 removed outlier: 6.502A pdb=" N ASP A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 617 through 620 removed outlier: 6.987A pdb=" N SER A 679 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LEU A 674 " --> pdb=" O SER A 679 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 617 through 620 removed outlier: 12.867A pdb=" N PHE A 682 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 11.089A pdb=" N ILE A 693 " --> pdb=" O PHE A 682 " (cutoff:3.500A) removed outlier: 10.485A pdb=" N VAL A 684 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N SER A 691 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR A 686 " --> pdb=" O ASN A 689 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.504A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 439 through 441 335 hydrogen bonds defined for protein. 951 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: 2.47 Time building geometry restraints manager: 3.05 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: 2301 1.34 - 1.46: 1884 1.46 - 1.58: 3124 1.58 - 1.70: 0 1.70 - 1.82: 62 Bond restraints: 7371 Sorted by residual: bond pdb=" N PRO A 424 " pdb=" CA PRO A 424 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.31e-02 5.83e+03 6.81e-01 bond pdb=" C PRO A 424 " pdb=" O PRO A 424 " ideal model delta sigma weight residual 1.246 1.239 0.006 8.50e-03 1.38e+04 5.22e-01 bond pdb=" CB PRO B 470 " pdb=" CG PRO B 470 " ideal model delta sigma weight residual 1.506 1.482 0.024 3.90e-02 6.57e+02 3.74e-01 bond pdb=" CG PRO A 499 " pdb=" CD PRO A 499 " ideal model delta sigma weight residual 1.503 1.483 0.020 3.40e-02 8.65e+02 3.56e-01 bond pdb=" C SER B 461 " pdb=" O SER B 461 " ideal model delta sigma weight residual 1.244 1.236 0.008 1.41e-02 5.03e+03 3.33e-01 ... (remaining 7366 not shown) Histogram of bond angle deviations from ideal: 99.64 - 106.51: 243 106.51 - 113.38: 3809 113.38 - 120.26: 2720 120.26 - 127.13: 3122 127.13 - 134.00: 108 Bond angle restraints: 10002 Sorted by residual: angle pdb=" CA LEU A 583 " pdb=" CB LEU A 583 " pdb=" CG LEU A 583 " ideal model delta sigma weight residual 116.30 123.39 -7.09 3.50e+00 8.16e-02 4.10e+00 angle pdb=" N GLU A 494 " pdb=" CA GLU A 494 " pdb=" C GLU A 494 " ideal model delta sigma weight residual 110.80 114.49 -3.69 2.13e+00 2.20e-01 3.01e+00 angle pdb=" N VAL A 363 " pdb=" CA VAL A 363 " pdb=" C VAL A 363 " ideal model delta sigma weight residual 109.34 112.94 -3.60 2.08e+00 2.31e-01 3.00e+00 angle pdb=" CA TYR A 384 " pdb=" CB TYR A 384 " pdb=" CG TYR A 384 " ideal model delta sigma weight residual 113.90 116.45 -2.55 1.80e+00 3.09e-01 2.00e+00 angle pdb=" N ASP A 493 " pdb=" CA ASP A 493 " pdb=" C ASP A 493 " ideal model delta sigma weight residual 107.48 110.64 -3.16 2.29e+00 1.91e-01 1.90e+00 ... (remaining 9997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4146 17.99 - 35.99: 187 35.99 - 53.98: 33 53.98 - 71.97: 12 71.97 - 89.96: 3 Dihedral angle restraints: 4381 sinusoidal: 1788 harmonic: 2593 Sorted by residual: dihedral pdb=" CA ASP A 493 " pdb=" C ASP A 493 " pdb=" N GLU A 494 " pdb=" CA GLU A 494 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA CYS A 343 " pdb=" CB CYS A 343 " pdb=" SG CYS A 343 " pdb=" SG CYS A 360 " ideal model delta sinusoidal sigma weight residual 79.00 19.07 59.93 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CA PRO A 135 " pdb=" C PRO A 135 " pdb=" N ASN A 136 " pdb=" CA ASN A 136 " ideal model delta harmonic sigma weight residual 180.00 162.79 17.21 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 4378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 555 0.026 - 0.052: 309 0.052 - 0.078: 99 0.078 - 0.104: 57 0.104 - 0.130: 14 Chirality restraints: 1034 Sorted by residual: chirality pdb=" CA ILE A 694 " pdb=" N ILE A 694 " pdb=" C ILE A 694 " pdb=" CB ILE A 694 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA VAL A 208 " pdb=" N VAL A 208 " pdb=" C VAL A 208 " pdb=" CB VAL A 208 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.93e-01 chirality pdb=" CA VAL B 369 " pdb=" N VAL B 369 " pdb=" C VAL B 369 " pdb=" CB VAL B 369 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.78e-01 ... (remaining 1031 not shown) Planarity restraints: 1293 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 387 " 0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO A 388 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 388 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 388 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 144 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO A 145 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 145 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 145 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 581 " 0.018 5.00e-02 4.00e+02 2.79e-02 1.24e+00 pdb=" N PRO A 582 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 582 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 582 " 0.016 5.00e-02 4.00e+02 ... (remaining 1290 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 60 2.59 - 3.17: 5886 3.17 - 3.75: 11309 3.75 - 4.32: 16500 4.32 - 4.90: 26677 Nonbonded interactions: 60432 Sorted by model distance: nonbonded pdb=" OE2 GLU A 401 " pdb="ZN ZN A 801 " model vdw 2.016 2.230 nonbonded pdb=" OG SER B 336 " pdb=" O LYS B 439 " model vdw 2.158 2.440 nonbonded pdb=" OD2 ASP B 393 " pdb=" OH TYR B 481 " model vdw 2.220 2.440 nonbonded pdb=" O VAL A 432 " pdb=" ND2 ASN A 436 " model vdw 2.233 2.520 nonbonded pdb=" OH TYR B 356 " pdb=" OD1 ASN B 375 " model vdw 2.239 2.440 ... (remaining 60427 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.820 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: 10.370 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.000 Find NCS groups from input model: 0.200 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:12.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 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 0.028 7371 Z= 0.173 Angle : 0.440 7.085 10002 Z= 0.222 Chirality : 0.039 0.130 1034 Planarity : 0.003 0.035 1293 Dihedral : 11.232 89.963 2702 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.87 % Allowed : 7.09 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.12 (0.27), residues: 875 helix: -0.14 (0.24), residues: 422 sheet: 1.68 (0.65), residues: 60 loop : -0.12 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 162 HIS 0.003 0.001 HIS A 240 PHE 0.008 0.001 PHE A 522 TYR 0.014 0.001 TYR A 384 ARG 0.002 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 155 time to evaluate : 0.906 Fit side-chains Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 303, in __init__ self.caller(self.optimize_sidechains) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable