Starting phenix.real_space_refine on Fri Oct 11 21:28:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zpb_60331/10_2024/8zpb_60331_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zpb_60331/10_2024/8zpb_60331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zpb_60331/10_2024/8zpb_60331.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zpb_60331/10_2024/8zpb_60331.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zpb_60331/10_2024/8zpb_60331_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zpb_60331/10_2024/8zpb_60331_trim.cif" } resolution = 2.6 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= 0.024 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: 8 Type Number sf(0) Gaussians P 1 5.49 5 S 24 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 3560 2.51 5 N 845 2.21 5 O 986 1.98 5 H 5257 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 10676 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 8801 Classifications: {'peptide': 551} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 530} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1779 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain breaks: 1 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 93 Unusual residues: {' CL': 1, ' NA': 2, 'LNR': 1, 'PTY': 1} Classifications: {'undetermined': 5, 'water': 51} Link IDs: {None: 55} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 5.33, per 1000 atoms: 0.50 Number of scatterers: 10676 At special positions: 0 Unit cell: (98.44, 74.52, 79.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Cl 1 17.00 S 24 16.00 P 1 15.00 Na 2 11.00 O 986 8.00 N 845 7.00 C 3560 6.00 H 5257 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 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: 2.73 Conformation dependent library (CDL) restraints added in 735.9 milliseconds 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1224 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 69.7% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 61 through 74 removed outlier: 3.631A pdb=" N PHE A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 81 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 121 removed outlier: 3.972A pdb=" N LEU A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) Proline residue: A 97 - end of helix removed outlier: 4.825A pdb=" N MET A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) Proline residue: A 108 - end of helix Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 134 through 166 removed outlier: 3.771A pdb=" N GLY A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 255 through 267 removed outlier: 4.207A pdb=" N SER A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TRP A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 282 removed outlier: 3.804A pdb=" N PHE A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.631A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 304 through 320 removed outlier: 4.205A pdb=" N TRP A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 338 through 372 Processing helix chain 'A' and resid 375 through 379 Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 389 through 397 Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.820A pdb=" N ASP A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 441 Processing helix chain 'A' and resid 441 through 458 Processing helix chain 'A' and resid 459 through 462 removed outlier: 3.688A pdb=" N THR A 462 " --> pdb=" O PHE A 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 459 through 462' Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.580A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 494 Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 567 removed outlier: 3.555A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 580 Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 594 through 597 Processing helix chain 'A' and resid 598 through 604 removed outlier: 4.399A pdb=" N ALA A 602 " --> pdb=" O HIS A 598 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN A 603 " --> pdb=" O HIS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 Processing helix chain 'A' and resid 610 through 615 removed outlier: 4.037A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57 removed outlier: 3.912A pdb=" N ARG A 56 " --> pdb=" O GLN B 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 544 through 545 Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.692A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 13 340 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: 3.72 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5250 1.03 - 1.23: 20 1.23 - 1.42: 2447 1.42 - 1.62: 3026 1.62 - 1.81: 39 Bond restraints: 10782 Sorted by residual: bond pdb=" CAE LNR A 701 " pdb=" CAI LNR A 701 " ideal model delta sigma weight residual 1.384 1.524 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" CAG LNR A 701 " pdb=" CAJ LNR A 701 " ideal model delta sigma weight residual 1.384 1.524 -0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" CAF LNR A 701 " pdb=" CAK LNR A 701 " ideal model delta sigma weight residual 1.386 1.524 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" CAI LNR A 701 " pdb=" CAJ LNR A 701 " ideal model delta sigma weight residual 1.402 1.317 0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" CAG LNR A 701 " pdb=" CAK LNR A 701 " ideal model delta sigma weight residual 1.395 1.316 0.079 2.00e-02 2.50e+03 1.55e+01 ... (remaining 10777 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 18221 1.14 - 2.28: 1067 2.28 - 3.42: 70 3.42 - 4.57: 19 4.57 - 5.71: 3 Bond angle restraints: 19380 Sorted by residual: angle pdb=" N MET A 107 " pdb=" CA MET A 107 " pdb=" C MET A 107 " ideal model delta sigma weight residual 112.75 108.87 3.88 1.36e+00 5.41e-01 8.15e+00 angle pdb=" CA SER A 182 " pdb=" C SER A 182 " pdb=" O SER A 182 " ideal model delta sigma weight residual 121.01 117.76 3.25 1.18e+00 7.18e-01 7.61e+00 angle pdb=" N PRO A 183 " pdb=" CA PRO A 183 " pdb=" C PRO A 183 " ideal model delta sigma weight residual 114.35 110.97 3.38 1.25e+00 6.40e-01 7.31e+00 angle pdb=" CA TRP A 80 " pdb=" C TRP A 80 " pdb=" O TRP A 80 " ideal model delta sigma weight residual 119.41 116.41 3.00 1.13e+00 7.83e-01 7.07e+00 angle pdb=" CA SER A 182 " pdb=" C SER A 182 " pdb=" N PRO A 183 " ideal model delta sigma weight residual 117.60 120.69 -3.09 1.18e+00 7.18e-01 6.85e+00 ... (remaining 19375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.82: 4766 23.82 - 47.64: 267 47.64 - 71.46: 85 71.46 - 95.28: 2 95.28 - 119.11: 1 Dihedral angle restraints: 5121 sinusoidal: 2620 harmonic: 2501 Sorted by residual: dihedral pdb=" N1 PTY A 705 " pdb=" C2 PTY A 705 " pdb=" C3 PTY A 705 " pdb=" O11 PTY A 705 " ideal model delta sinusoidal sigma weight residual 65.33 -175.56 -119.11 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" CA ILE B 51 " pdb=" C ILE B 51 " pdb=" N GLN B 52 " pdb=" CA GLN B 52 " ideal model delta harmonic sigma weight residual -180.00 -162.11 -17.89 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA TRP A 128 " pdb=" C TRP A 128 " pdb=" N LYS A 129 " pdb=" CA LYS A 129 " ideal model delta harmonic sigma weight residual 180.00 164.13 15.87 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 5118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 665 0.046 - 0.091: 129 0.091 - 0.137: 30 0.137 - 0.182: 1 0.182 - 0.228: 1 Chirality restraints: 826 Sorted by residual: chirality pdb=" CAL LNR A 701 " pdb=" CAH LNR A 701 " pdb=" CAK LNR A 701 " pdb=" OAD LNR A 701 " both_signs ideal model delta sigma weight residual False -2.28 -2.51 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA VAL A 79 " pdb=" N VAL A 79 " pdb=" C VAL A 79 " pdb=" CB VAL A 79 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CA VAL B 2 " pdb=" N VAL B 2 " pdb=" C VAL B 2 " pdb=" CB VAL B 2 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 823 not shown) Planarity restraints: 1563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 102 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.09e+00 pdb=" C LEU A 102 " 0.035 2.00e-02 2.50e+03 pdb=" O LEU A 102 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE A 103 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 213 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.33e+00 pdb=" C PHE A 213 " -0.026 2.00e-02 2.50e+03 pdb=" O PHE A 213 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR A 214 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 391 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.98e+00 pdb=" N PRO A 392 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 392 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 392 " -0.020 5.00e-02 4.00e+02 ... (remaining 1560 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 629 2.19 - 2.79: 21815 2.79 - 3.39: 32592 3.39 - 4.00: 43958 4.00 - 4.60: 68263 Nonbonded interactions: 167257 Sorted by model distance: nonbonded pdb=" O GLN B 52 " pdb="HH22 ARG B 71 " model vdw 1.582 2.450 nonbonded pdb=" OE2 GLU B 6 " pdb=" H CYS B 95 " model vdw 1.602 2.450 nonbonded pdb=" O PHE A 495 " pdb="HE21 GLN A 608 " model vdw 1.609 2.450 nonbonded pdb=" OE1 GLU B 6 " pdb=" H GLY B 113 " model vdw 1.655 2.450 nonbonded pdb="HH22 ARG A 81 " pdb=" O HOH A 810 " model vdw 1.663 2.450 ... (remaining 167252 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: 1.560 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: 0.180 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 25.570 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:11.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.0000 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: