Starting phenix.real_space_refine on Sun Jun 15 08:43:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dpb_47101/06_2025/9dpb_47101.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dpb_47101/06_2025/9dpb_47101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dpb_47101/06_2025/9dpb_47101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dpb_47101/06_2025/9dpb_47101.map" model { file = "/net/cci-nas-00/data/ceres_data/9dpb_47101/06_2025/9dpb_47101.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dpb_47101/06_2025/9dpb_47101.cif" } resolution = 2.9 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= 0.007 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 9120 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 P 79 5.49 5 Mg 4 5.21 5 S 56 5.16 5 Na 1 4.78 5 C 5970 2.51 5 N 1680 2.21 5 O 2046 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9836 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 4100 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 29, 'TRANS': 476} Chain: "B" Number of atoms: 4092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 4092 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 29, 'TRANS': 475} Chain: "C" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1557 Classifications: {'RNA': 73} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 4, 'rna3p_pur': 29, 'rna3p_pyr': 32} Link IDs: {'rna2p': 11, 'rna3p': 61} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'APC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'APC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.36, per 1000 atoms: 0.65 Number of scatterers: 9836 At special positions: 0 Unit cell: (85.6, 103.79, 141.24, 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) S 56 16.00 P 79 15.00 Mg 4 11.99 Na 1 11.00 O 2046 8.00 N 1680 7.00 C 5970 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: 2.44 Conformation dependent library (CDL) restraints added in 1.1 seconds 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1898 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 10 sheets defined 38.7% alpha, 24.1% beta 26 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 3.09 Creating SS restraints... Processing helix chain 'A' and resid 75 through 90 Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 238 through 261 removed outlier: 3.782A pdb=" N GLN A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 311 Processing helix chain 'A' and resid 346 through 367 removed outlier: 4.300A pdb=" N GLU A 352 " --> pdb=" O HIS A 348 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE A 353 " --> pdb=" O ASP A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 405 Processing helix chain 'A' and resid 410 through 415 removed outlier: 4.466A pdb=" N GLU A 415 " --> pdb=" O ASN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 430 Processing helix chain 'A' and resid 439 through 452 Processing helix chain 'A' and resid 453 through 456 Processing helix chain 'A' and resid 504 through 521 Processing helix chain 'A' and resid 530 through 538 removed outlier: 3.724A pdb=" N GLU A 538 " --> pdb=" O CYS A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 559 Processing helix chain 'A' and resid 563 through 567 Processing helix chain 'B' and resid 73 through 90 removed outlier: 3.533A pdb=" N ASN B 90 " --> pdb=" O GLN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.669A pdb=" N ASN B 174 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 229 Processing helix chain 'B' and resid 229 through 237 Processing helix chain 'B' and resid 238 through 261 removed outlier: 3.614A pdb=" N GLN B 242 " --> pdb=" O ASP B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 311 Processing helix chain 'B' and resid 348 through 367 removed outlier: 4.435A pdb=" N GLU B 352 " --> pdb=" O HIS B 348 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE B 353 " --> pdb=" O ASP B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 405 Processing helix chain 'B' and resid 416 through 430 removed outlier: 3.538A pdb=" N ARG B 420 " --> pdb=" O THR B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 452 Processing helix chain 'B' and resid 468 through 470 No H-bonds generated for 'chain 'B' and resid 468 through 470' Processing helix chain 'B' and resid 504 through 522 Processing helix chain 'B' and resid 530 through 539 Processing helix chain 'B' and resid 551 through 559 Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 137 removed outlier: 5.862A pdb=" N ILE A 132 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG A 148 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA A 134 " --> pdb=" O ASP A 146 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N LYS A 153 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N ILE A 198 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLN A 155 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N MET A 157 " --> pdb=" O PRO A 200 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N GLU A 202 " --> pdb=" O MET A 157 " (cutoff:3.500A) removed outlier: 10.160A pdb=" N ASN A 159 " --> pdb=" O GLU A 202 " (cutoff:3.500A) removed outlier: 12.610A pdb=" N THR A 204 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE A 198 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY A 189 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASN A 187 " --> pdb=" O PRO A 200 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE A 181 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 264 through 265 removed outlier: 5.932A pdb=" N LEU A 264 " --> pdb=" O TYR A 316 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N ILE A 318 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE A 495 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N GLU A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL A 490 " --> pdb=" O GLU A 494 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS A 496 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ARG A 392 " --> pdb=" O PHE A 461 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 271 through 272 Processing sheet with id=AA4, first strand: chain 'A' and resid 370 through 373 Processing sheet with id=AA5, first strand: chain 'A' and resid 465 through 466 removed outlier: 3.889A pdb=" N HIS A 465 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 159 removed outlier: 3.919A pdb=" N ALA B 134 " --> pdb=" O ASP B 146 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARG B 148 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ILE B 132 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE B 181 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU B 205 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY B 183 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILE B 203 " --> pdb=" O GLY B 183 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLN B 185 " --> pdb=" O TYR B 201 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 264 through 265 removed outlier: 5.854A pdb=" N LEU B 264 " --> pdb=" O TYR B 316 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ILE B 318 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 495 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N GLU B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL B 490 " --> pdb=" O GLU B 494 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N CYS B 496 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLU B 484 " --> pdb=" O THR B 500 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG B 392 " --> pdb=" O PHE B 461 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 264 through 265 removed outlier: 5.854A pdb=" N LEU B 264 " --> pdb=" O TYR B 316 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ILE B 318 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 495 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N GLU B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL B 490 " --> pdb=" O GLU B 494 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N CYS B 496 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLU B 484 " --> pdb=" O THR B 500 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N HIS B 465 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 271 through 272 Processing sheet with id=AB1, first strand: chain 'B' and resid 370 through 373 388 hydrogen bonds defined for protein. 1119 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 3.18 Time building geometry restraints manager: 2.81 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: 2116 1.33 - 1.45: 2612 1.45 - 1.58: 5230 1.58 - 1.70: 151 1.70 - 1.82: 100 Bond restraints: 10209 Sorted by residual: bond pdb=" C PRO B 375 " pdb=" N ASP B 376 " ideal model delta sigma weight residual 1.332 1.207 0.125 1.40e-02 5.10e+03 7.99e+01 bond pdb=" C GLY B 405 " pdb=" N MET B 406 " ideal model delta sigma weight residual 1.330 1.407 -0.077 1.53e-02 4.27e+03 2.56e+01 bond pdb=" C THR B 191 " pdb=" N LYS B 192 " ideal model delta sigma weight residual 1.335 1.401 -0.066 1.31e-02 5.83e+03 2.56e+01 bond pdb=" C GLY A 405 " pdb=" N MET A 406 " ideal model delta sigma weight residual 1.329 1.398 -0.068 1.36e-02 5.41e+03 2.51e+01 bond pdb=" C LYS B 135 " pdb=" N ARG B 136 " ideal model delta sigma weight residual 1.330 1.396 -0.065 1.45e-02 4.76e+03 2.03e+01 ... (remaining 10204 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.27: 14139 5.27 - 10.54: 17 10.54 - 15.81: 2 15.81 - 21.08: 0 21.08 - 26.35: 2 Bond angle restraints: 14160 Sorted by residual: angle pdb=" PB APC B 602 " pdb=" O3B APC B 602 " pdb=" PG APC B 602 " ideal model delta sigma weight residual 106.84 133.19 -26.35 3.00e+00 1.11e-01 7.72e+01 angle pdb=" PB APC A 602 " pdb=" O3B APC A 602 " pdb=" PG APC A 602 " ideal model delta sigma weight residual 106.84 131.47 -24.63 3.00e+00 1.11e-01 6.74e+01 angle pdb=" O PRO B 375 " pdb=" C PRO B 375 " pdb=" N ASP B 376 " ideal model delta sigma weight residual 122.38 115.08 7.30 1.39e+00 5.18e-01 2.76e+01 angle pdb=" C5' APC B 602 " pdb=" O5' APC B 602 " pdb=" PA APC B 602 " ideal model delta sigma weight residual 106.85 122.55 -15.70 3.00e+00 1.11e-01 2.74e+01 angle pdb=" C5' APC A 602 " pdb=" O5' APC A 602 " pdb=" PA APC A 602 " ideal model delta sigma weight residual 106.85 122.21 -15.36 3.00e+00 1.11e-01 2.62e+01 ... (remaining 14155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.38: 5881 32.38 - 64.76: 412 64.76 - 97.14: 40 97.14 - 129.52: 2 129.52 - 161.90: 1 Dihedral angle restraints: 6336 sinusoidal: 3385 harmonic: 2951 Sorted by residual: dihedral pdb=" O4' U C 20 " pdb=" C1' U C 20 " pdb=" N1 U C 20 " pdb=" C2 U C 20 " ideal model delta sinusoidal sigma weight residual 200.00 38.10 161.90 1 1.50e+01 4.44e-03 8.32e+01 dihedral pdb=" CA ILE A 462 " pdb=" C ILE A 462 " pdb=" N CYS A 463 " pdb=" CA CYS A 463 " ideal model delta harmonic sigma weight residual 180.00 -156.15 -23.85 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA TYR B 499 " pdb=" C TYR B 499 " pdb=" N THR B 500 " pdb=" CA THR B 500 " ideal model delta harmonic sigma weight residual 180.00 156.70 23.30 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 6333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1316 0.050 - 0.100: 228 0.100 - 0.150: 44 0.150 - 0.200: 8 0.200 - 0.250: 2 Chirality restraints: 1598 Sorted by residual: chirality pdb=" CG LEU B 329 " pdb=" CB LEU B 329 " pdb=" CD1 LEU B 329 " pdb=" CD2 LEU B 329 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CG LEU A 444 " pdb=" CB LEU A 444 " pdb=" CD1 LEU A 444 " pdb=" CD2 LEU A 444 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE B 462 " pdb=" N ILE B 462 " pdb=" C ILE B 462 " pdb=" CB ILE B 462 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.79e-01 ... (remaining 1595 not shown) Planarity restraints: 1549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 376 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.03e+00 pdb=" C ASP B 376 " 0.052 2.00e-02 2.50e+03 pdb=" O ASP B 376 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY B 377 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 388 " -0.032 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO A 389 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 389 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 389 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 468 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.18e+00 pdb=" C ILE B 468 " -0.031 2.00e-02 2.50e+03 pdb=" O ILE B 468 " 0.012 2.00e-02 2.50e+03 pdb=" N MET B 469 " 0.010 2.00e-02 2.50e+03 ... (remaining 1546 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1668 2.76 - 3.30: 9423 3.30 - 3.83: 17982 3.83 - 4.37: 21263 4.37 - 4.90: 34339 Nonbonded interactions: 84675 Sorted by model distance: nonbonded pdb=" N GLU B 195 " pdb=" OE1 GLU B 195 " model vdw 2.231 3.120 nonbonded pdb=" N GLU A 453 " pdb=" OE1 GLU A 453 " model vdw 2.252 3.120 nonbonded pdb=" OD2 ASP B 222 " pdb=" OG1 THR B 225 " model vdw 2.258 3.040 nonbonded pdb=" OE2 GLU A 494 " pdb="MG MG A 603 " model vdw 2.258 2.170 nonbonded pdb=" OH TYR B 286 " pdb=" OD1 ASP B 291 " model vdw 2.279 3.040 ... (remaining 84670 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 72 through 576 or resid 601 or resid 602 through 604)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.050 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:11.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 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 : 0.005 0.125 10209 Z= 0.318 Angle : 0.770 26.351 14160 Z= 0.437 Chirality : 0.041 0.250 1598 Planarity : 0.005 0.048 1549 Dihedral : 19.843 161.904 4438 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.45 % Allowed : 22.19 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.27), residues: 1007 helix: 0.88 (0.27), residues: 366 sheet: -0.28 (0.36), residues: 211 loop : -1.06 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 547 HIS 0.011 0.001 HIS B 465 PHE 0.026 0.001 PHE B 340 TYR 0.010 0.001 TYR A 316 ARG 0.006 0.000 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.11241 ( 431) hydrogen bonds : angle 6.44685 ( 1227) covalent geometry : bond 0.00504 (10209) covalent geometry : angle 0.76951 (14160) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: A 469 MET cc_start: 0.8014 (mpt) cc_final: 0.7776 (mpt) outliers start: 13 outliers final: 10 residues processed: 87 average time/residue: 1.3601 time to fit residues: 126.8984 Evaluate side-chains 71 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 529 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 229 GLN A 288 ASN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.114206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.069028 restraints weight = 18366.396| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.69 r_work: 0.2880 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10209 Z= 0.229 Angle : 0.581 8.737 14160 Z= 0.295 Chirality : 0.040 0.297 1598 Planarity : 0.005 0.051 1549 Dihedral : 19.473 161.880 2350 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.34 % Allowed : 20.51 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.27), residues: 1007 helix: 1.19 (0.27), residues: 370 sheet: -0.36 (0.37), residues: 217 loop : -0.89 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 547 HIS 0.004 0.001 HIS A 215 PHE 0.032 0.002 PHE A 340 TYR 0.012 0.002 TYR A 316 ARG 0.004 0.001 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.04726 ( 431) hydrogen bonds : angle 5.12167 ( 1227) covalent geometry : bond 0.00543 (10209) covalent geometry : angle 0.58141 (14160) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 70 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: A 301 GLU cc_start: 0.8773 (tt0) cc_final: 0.8290 (tp30) REVERT: A 453 GLU cc_start: 0.7994 (mp0) cc_final: 0.7763 (mp0) REVERT: A 499 TYR cc_start: 0.8275 (m-80) cc_final: 0.7996 (m-80) REVERT: B 161 ARG cc_start: 0.8795 (mtm-85) cc_final: 0.8556 (mtm-85) REVERT: B 192 LYS cc_start: 0.9129 (ttpp) cc_final: 0.8771 (tmmt) outliers start: 30 outliers final: 11 residues processed: 93 average time/residue: 1.2835 time to fit residues: 129.0047 Evaluate side-chains 75 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 469 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 4 optimal weight: 0.0050 chunk 89 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 97 optimal weight: 0.0770 chunk 48 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 overall best weight: 0.5352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.118025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.073888 restraints weight = 18768.445| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.63 r_work: 0.3045 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10209 Z= 0.106 Angle : 0.518 7.916 14160 Z= 0.258 Chirality : 0.036 0.149 1598 Planarity : 0.004 0.048 1549 Dihedral : 19.231 163.164 2336 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.57 % Allowed : 20.07 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.27), residues: 1007 helix: 1.36 (0.27), residues: 371 sheet: -0.28 (0.36), residues: 215 loop : -0.85 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 547 HIS 0.002 0.000 HIS A 465 PHE 0.027 0.001 PHE B 340 TYR 0.014 0.001 TYR A 499 ARG 0.003 0.000 ARG A 442 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 431) hydrogen bonds : angle 4.75262 ( 1227) covalent geometry : bond 0.00247 (10209) covalent geometry : angle 0.51838 (14160) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8285 (m-30) REVERT: A 301 GLU cc_start: 0.8692 (tt0) cc_final: 0.8283 (tp30) REVERT: A 450 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8317 (mp0) REVERT: A 453 GLU cc_start: 0.7986 (mp0) cc_final: 0.7602 (mp0) REVERT: A 499 TYR cc_start: 0.8215 (m-80) cc_final: 0.7960 (m-80) REVERT: B 161 ARG cc_start: 0.8700 (mtm-85) cc_final: 0.8336 (mtm-85) REVERT: B 162 ASN cc_start: 0.9090 (m110) cc_final: 0.8255 (m110) REVERT: B 192 LYS cc_start: 0.9091 (ttpp) cc_final: 0.8798 (tmmt) REVERT: B 406 MET cc_start: 0.7361 (pp-130) cc_final: 0.6427 (pmm) outliers start: 32 outliers final: 12 residues processed: 92 average time/residue: 1.2980 time to fit residues: 128.5793 Evaluate side-chains 75 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 51.3899 > 50: distance: 43 - 75: 13.975 distance: 50 - 55: 7.388 distance: 51 - 84: 4.835 distance: 55 - 56: 8.743 distance: 56 - 59: 3.027 distance: 57 - 58: 20.726 distance: 57 - 66: 26.392 distance: 58 - 95: 25.165 distance: 59 - 60: 13.508 distance: 60 - 61: 18.892 distance: 61 - 62: 12.461 distance: 62 - 63: 10.712 distance: 63 - 64: 12.291 distance: 63 - 65: 9.779 distance: 66 - 67: 22.236 distance: 67 - 68: 13.082 distance: 67 - 70: 17.221 distance: 68 - 69: 6.289 distance: 68 - 75: 6.824 distance: 69 - 103: 21.589 distance: 70 - 71: 10.635 distance: 71 - 72: 22.184 distance: 72 - 73: 29.102 distance: 72 - 74: 30.981 distance: 75 - 76: 4.485 distance: 76 - 77: 6.682 distance: 76 - 79: 4.385 distance: 77 - 78: 5.267 distance: 77 - 84: 4.899 distance: 78 - 111: 11.154 distance: 79 - 80: 8.392 distance: 80 - 81: 21.566 distance: 81 - 82: 20.918 distance: 82 - 83: 16.583 distance: 84 - 85: 6.528 distance: 85 - 86: 3.265 distance: 85 - 88: 8.722 distance: 86 - 95: 6.273 distance: 87 - 122: 5.587 distance: 88 - 89: 6.873 distance: 89 - 90: 7.070 distance: 89 - 91: 3.100 distance: 90 - 92: 5.846 distance: 91 - 93: 8.918 distance: 92 - 94: 5.331 distance: 93 - 94: 4.299 distance: 95 - 96: 7.171 distance: 96 - 97: 4.573 distance: 96 - 99: 5.329 distance: 97 - 98: 6.096 distance: 97 - 103: 6.516 distance: 98 - 128: 11.609 distance: 99 - 100: 10.129 distance: 99 - 101: 8.230 distance: 103 - 104: 5.575 distance: 104 - 105: 9.949 distance: 104 - 107: 7.218 distance: 105 - 106: 12.138 distance: 105 - 111: 4.681 distance: 106 - 137: 9.768 distance: 107 - 108: 11.743 distance: 107 - 109: 9.615 distance: 108 - 110: 14.201 distance: 111 - 112: 3.081 distance: 112 - 113: 4.540 distance: 112 - 115: 6.782 distance: 113 - 122: 3.192 distance: 115 - 116: 5.966 distance: 116 - 117: 9.851 distance: 117 - 118: 5.850 distance: 118 - 119: 4.257 distance: 119 - 120: 4.640 distance: 119 - 121: 20.300 distance: 122 - 123: 7.082 distance: 123 - 124: 6.628 distance: 123 - 126: 8.218 distance: 124 - 125: 5.602 distance: 124 - 128: 3.923 distance: 125 - 153: 8.566 distance: 126 - 127: 15.732 distance: 128 - 129: 3.636 distance: 129 - 130: 3.529 distance: 129 - 132: 6.794 distance: 130 - 131: 9.375 distance: 131 - 160: 6.914 distance: 132 - 133: 11.066 distance: 133 - 134: 5.317 distance: 134 - 135: 3.926 distance: 135 - 136: 8.347 distance: 137 - 138: 6.122 distance: 138 - 139: 4.824 distance: 139 - 140: 4.067 distance: 139 - 145: 3.585 distance: 140 - 165: 10.094 distance: 141 - 143: 7.317 distance: 142 - 144: 9.830