Starting phenix.real_space_refine on Sun Feb 18 10:09:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpf_29362/02_2024/8fpf_29362_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpf_29362/02_2024/8fpf_29362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpf_29362/02_2024/8fpf_29362.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpf_29362/02_2024/8fpf_29362.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpf_29362/02_2024/8fpf_29362_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fpf_29362/02_2024/8fpf_29362_trim_updated.pdb" } resolution = 3.27 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= 0.027 sd= 0.067 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: 6 Type Number sf(0) Gaussians P 21 5.49 5 S 39 5.16 5 C 6982 2.51 5 N 1659 2.21 5 O 1923 1.98 5 H 9854 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20478 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 10708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 10708 Classifications: {'peptide': 666} Link IDs: {'PTRANS': 13, 'TRANS': 652} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 8861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 8861 Classifications: {'peptide': 558} Link IDs: {'PTRANS': 19, 'TRANS': 538} Chain breaks: 1 Chain: "D" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 493 Unusual residues: {'ATP': 1, 'POV': 14} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 331 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'POV:plan-3': 6, 'POV:plan-2': 5, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 416 Unusual residues: {'ATP': 1, 'POV': 11} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 236 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 3, 'POV:plan-1': 4} Unresolved non-hydrogen planarities: 25 Time building chain proxies: 9.59, per 1000 atoms: 0.47 Number of scatterers: 20478 At special positions: 0 Unit cell: (75.9, 105.6, 159.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 39 16.00 P 21 15.00 O 1923 8.00 N 1659 7.00 C 6982 6.00 H 9854 1.00 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 - 3.50 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: 17.54 Conformation dependent library (CDL) restraints added in 2.2 seconds 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2270 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 8 sheets defined 59.0% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.66 Creating SS restraints... Processing helix chain 'D' and resid 3 through 12 Processing helix chain 'D' and resid 15 through 51 Proline residue: D 36 - end of helix removed outlier: 3.721A pdb=" N HIS D 46 " --> pdb=" O MET D 42 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY D 49 " --> pdb=" O ASP D 45 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE D 50 " --> pdb=" O HIS D 46 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLU D 51 " --> pdb=" O ILE D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 195 Proline residue: D 144 - end of helix removed outlier: 4.830A pdb=" N LYS D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLY D 148 " --> pdb=" O PRO D 144 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE D 165 " --> pdb=" O VAL D 161 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE D 166 " --> pdb=" O PHE D 162 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR D 168 " --> pdb=" O VAL D 164 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'D' and resid 198 through 202 Processing helix chain 'D' and resid 206 through 248 removed outlier: 3.666A pdb=" N VAL D 210 " --> pdb=" O ALA D 206 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP D 216 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR D 217 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR D 233 " --> pdb=" O SER D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 296 removed outlier: 3.809A pdb=" N VAL D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE D 259 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N VAL D 260 " --> pdb=" O ALA D 256 " (cutoff:3.500A) Proline residue: D 261 - end of helix removed outlier: 4.201A pdb=" N TYR D 276 " --> pdb=" O ARG D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 304 Processing helix chain 'D' and resid 308 through 335 Processing helix chain 'D' and resid 339 through 361 Processing helix chain 'D' and resid 369 through 382 Processing helix chain 'D' and resid 384 through 410 removed outlier: 4.328A pdb=" N THR D 387 " --> pdb=" O GLN D 384 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY D 388 " --> pdb=" O PRO D 385 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN D 392 " --> pdb=" O ILE D 389 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU D 396 " --> pdb=" O PHE D 393 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU D 397 " --> pdb=" O SER D 394 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU D 398 " --> pdb=" O LYS D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 476 Processing helix chain 'D' and resid 494 through 496 No H-bonds generated for 'chain 'D' and resid 494 through 496' Processing helix chain 'D' and resid 499 through 505 removed outlier: 3.529A pdb=" N HIS D 505 " --> pdb=" O GLU D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 535 through 541 Processing helix chain 'D' and resid 546 through 549 No H-bonds generated for 'chain 'D' and resid 546 through 549' Processing helix chain 'D' and resid 569 through 583 Processing helix chain 'D' and resid 603 through 613 Processing helix chain 'D' and resid 648 through 653 Processing helix chain 'D' and resid 656 through 664 Processing helix chain 'C' and resid 4 through 7 No H-bonds generated for 'chain 'C' and resid 4 through 7' Processing helix chain 'C' and resid 9 through 14 Processing helix chain 'C' and resid 17 through 34 Processing helix chain 'C' and resid 36 through 48 Processing helix chain 'C' and resid 54 through 102 Processing helix chain 'C' and resid 106 through 111 Processing helix chain 'C' and resid 114 through 122 Processing helix chain 'C' and resid 124 through 156 removed outlier: 4.357A pdb=" N ILE C 136 " --> pdb=" O THR C 132 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N MET C 146 " --> pdb=" O SER C 142 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET C 147 " --> pdb=" O THR C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 165 Processing helix chain 'C' and resid 167 through 206 removed outlier: 4.346A pdb=" N VAL C 171 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU C 202 " --> pdb=" O ASN C 198 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU C 203 " --> pdb=" O ASP C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 217 through 270 removed outlier: 3.878A pdb=" N ILE C 241 " --> pdb=" O LYS C 237 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU C 244 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE C 245 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLU C 246 " --> pdb=" O ASP C 242 " (cutoff:3.500A) Proline residue: C 247 - end of helix removed outlier: 3.747A pdb=" N SER C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 288 Processing helix chain 'C' and resid 291 through 317 removed outlier: 3.883A pdb=" N GLY C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU C 314 " --> pdb=" O ASP C 310 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 382 No H-bonds generated for 'chain 'C' and resid 379 through 382' Processing helix chain 'C' and resid 407 through 413 Processing helix chain 'C' and resid 428 through 433 Processing helix chain 'C' and resid 442 through 450 removed outlier: 3.706A pdb=" N GLN C 446 " --> pdb=" O GLU C 443 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU C 450 " --> pdb=" O ALA C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 458 Processing helix chain 'C' and resid 479 through 491 removed outlier: 4.005A pdb=" N ALA C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 520 Processing helix chain 'C' and resid 534 through 536 No H-bonds generated for 'chain 'C' and resid 534 through 536' Processing helix chain 'C' and resid 556 through 561 Processing sheet with id= A, first strand: chain 'D' and resid 54 through 57 removed outlier: 4.336A pdb=" N SER D 71 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 89 through 93 Processing sheet with id= C, first strand: chain 'D' and resid 116 through 119 removed outlier: 3.891A pdb=" N ILE D 119 " --> pdb=" O ARG D 126 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG D 126 " --> pdb=" O ILE D 119 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 430 through 433 Processing sheet with id= E, first strand: chain 'D' and resid 506 through 509 removed outlier: 6.616A pdb=" N ILE D 587 " --> pdb=" O GLY D 507 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL D 509 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE D 589 " --> pdb=" O VAL D 509 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N THR D 617 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N LEU D 590 " --> pdb=" O THR D 617 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N PHE D 619 " --> pdb=" O LEU D 590 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'D' and resid 634 through 636 Processing sheet with id= G, first strand: chain 'C' and resid 337 through 339 Processing sheet with id= H, first strand: chain 'C' and resid 549 through 554 removed outlier: 7.147A pdb=" N VAL C 544 " --> pdb=" O ALA C 551 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ARG C 553 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE C 542 " --> pdb=" O ARG C 553 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR C 526 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ILE C 369 " --> pdb=" O THR C 526 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE C 528 " --> pdb=" O ILE C 369 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1503 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: 6.91 Time building geometry restraints manager: 18.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 3240 1.05 - 1.24: 7891 1.24 - 1.43: 3002 1.43 - 1.62: 6433 1.62 - 1.81: 78 Bond restraints: 20644 Sorted by residual: bond pdb=" NE1 TRP D 8 " pdb=" HE1 TRP D 8 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP D 264 " pdb=" HE1 TRP D 264 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP C 78 " pdb=" HE1 TRP C 78 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP D 54 " pdb=" HE1 TRP D 54 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" NE1 TRP C 565 " pdb=" HE1 TRP C 565 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 ... (remaining 20639 not shown) Histogram of bond angle deviations from ideal: 99.41 - 106.35: 395 106.35 - 113.29: 23722 113.29 - 120.22: 6985 120.22 - 127.16: 5552 127.16 - 134.10: 94 Bond angle restraints: 36748 Sorted by residual: angle pdb=" PB ATP C 612 " pdb=" O3B ATP C 612 " pdb=" PG ATP C 612 " ideal model delta sigma weight residual 139.87 122.28 17.59 1.00e+00 1.00e+00 3.09e+02 angle pdb=" PB ATP D 715 " pdb=" O3B ATP D 715 " pdb=" PG ATP D 715 " ideal model delta sigma weight residual 139.87 128.91 10.96 1.00e+00 1.00e+00 1.20e+02 angle pdb=" PA ATP C 612 " pdb=" O3A ATP C 612 " pdb=" PB ATP C 612 " ideal model delta sigma weight residual 136.83 127.46 9.37 1.00e+00 1.00e+00 8.77e+01 angle pdb=" PA ATP D 715 " pdb=" O3A ATP D 715 " pdb=" PB ATP D 715 " ideal model delta sigma weight residual 136.83 128.64 8.19 1.00e+00 1.00e+00 6.70e+01 angle pdb=" N LEU D 257 " pdb=" CA LEU D 257 " pdb=" C LEU D 257 " ideal model delta sigma weight residual 112.89 104.47 8.42 1.24e+00 6.50e-01 4.61e+01 ... (remaining 36743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.31: 9527 35.31 - 70.63: 350 70.63 - 105.94: 45 105.94 - 141.25: 24 141.25 - 176.56: 4 Dihedral angle restraints: 9950 sinusoidal: 5737 harmonic: 4213 Sorted by residual: dihedral pdb=" C27 POV C 609 " pdb=" C28 POV C 609 " pdb=" C29 POV C 609 " pdb="C210 POV C 609 " ideal model delta sinusoidal sigma weight residual 127.48 -49.08 176.56 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C29 POV D 704 " pdb="C210 POV D 704 " pdb="C211 POV D 704 " pdb="C212 POV D 704 " ideal model delta sinusoidal sigma weight residual 112.25 -57.35 169.60 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C27 POV D 707 " pdb=" C28 POV D 707 " pdb=" C29 POV D 707 " pdb="C210 POV D 707 " ideal model delta sinusoidal sigma weight residual 127.48 -64.65 -167.87 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 9947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1075 0.037 - 0.074: 319 0.074 - 0.111: 99 0.111 - 0.147: 38 0.147 - 0.184: 12 Chirality restraints: 1543 Sorted by residual: chirality pdb=" CB ILE C 369 " pdb=" CA ILE C 369 " pdb=" CG1 ILE C 369 " pdb=" CG2 ILE C 369 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.49e-01 chirality pdb=" CA ILE D 642 " pdb=" N ILE D 642 " pdb=" C ILE D 642 " pdb=" CB ILE D 642 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" CA LEU C 529 " pdb=" N LEU C 529 " pdb=" C LEU C 529 " pdb=" CB LEU C 529 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.03e-01 ... (remaining 1540 not shown) Planarity restraints: 2940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV D 712 " -0.264 2.00e-02 2.50e+03 2.49e-01 6.20e+02 pdb=" C29 POV D 712 " 0.317 2.00e-02 2.50e+03 pdb="C210 POV D 712 " 0.169 2.00e-02 2.50e+03 pdb="C211 POV D 712 " -0.222 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 710 " -0.182 2.00e-02 2.50e+03 2.02e-01 4.07e+02 pdb=" C29 POV D 710 " 0.139 2.00e-02 2.50e+03 pdb="C210 POV D 710 " 0.255 2.00e-02 2.50e+03 pdb="C211 POV D 710 " -0.213 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C 605 " 0.089 2.00e-02 2.50e+03 1.99e-01 3.95e+02 pdb=" C29 POV C 605 " -0.262 2.00e-02 2.50e+03 pdb="C210 POV C 605 " 0.269 2.00e-02 2.50e+03 pdb="C211 POV C 605 " -0.095 2.00e-02 2.50e+03 ... (remaining 2937 not shown) Histogram of nonbonded interaction distances: 1.32 - 1.97: 303 1.97 - 2.63: 24359 2.63 - 3.29: 59448 3.29 - 3.94: 76158 3.94 - 4.60: 116832 Nonbonded interactions: 277100 Sorted by model distance: nonbonded pdb=" H ALA D 482 " pdb=" HH TYR D 495 " model vdw 1.317 2.100 nonbonded pdb="HD13 ILE D 302 " pdb=" HH TYR C 434 " model vdw 1.400 2.270 nonbonded pdb=" HG2 GLU D 420 " pdb=" HG SER D 498 " model vdw 1.452 2.270 nonbonded pdb=" HZ3 LYS D 607 " pdb="HG21 VAL D 611 " model vdw 1.470 2.270 nonbonded pdb=" HB3 ALA D 58 " pdb=" HZ3 LYS D 62 " model vdw 1.487 2.270 ... (remaining 277095 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: 1.310 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: 0.340 Extract box with map and model: 6.730 Check model and map are aligned: 0.330 Set scattering table: 0.190 Process input model: 68.710 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 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 : 0.008 0.083 10790 Z= 0.473 Angle : 0.895 17.592 14403 Z= 0.551 Chirality : 0.044 0.184 1543 Planarity : 0.015 0.249 1752 Dihedral : 20.445 176.563 4375 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % 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: -0.57 (0.24), residues: 1218 helix: 0.62 (0.19), residues: 735 sheet: -0.54 (0.73), residues: 63 loop : -2.16 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 78 HIS 0.005 0.001 HIS C 80 PHE 0.027 0.002 PHE D 577 TYR 0.022 0.002 TYR D 98 ARG 0.007 0.001 ARG D 645 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 ASN cc_start: 0.6256 (t0) cc_final: 0.5771 (t0) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.5719 time to fit residues: 88.2375 Evaluate side-chains 87 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 452 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10790 Z= 0.199 Angle : 0.540 8.133 14403 Z= 0.293 Chirality : 0.037 0.148 1543 Planarity : 0.005 0.047 1752 Dihedral : 22.176 178.873 2064 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.96 % Allowed : 5.11 % Favored : 93.93 % 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: -0.22 (0.24), residues: 1218 helix: 0.93 (0.19), residues: 741 sheet: -0.42 (0.73), residues: 64 loop : -2.11 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 78 HIS 0.003 0.001 HIS C 80 PHE 0.015 0.001 PHE D 323 TYR 0.011 0.001 TYR C 434 ARG 0.004 0.000 ARG C 311 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 ASN cc_start: 0.6166 (t0) cc_final: 0.5703 (t0) outliers start: 10 outliers final: 6 residues processed: 98 average time/residue: 0.5739 time to fit residues: 78.6222 Evaluate side-chains 95 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 506 MET Chi-restraints excluded: chain C residue 341 HIS Chi-restraints excluded: chain C residue 448 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 110 optimal weight: 0.4980 chunk 118 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 GLN ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10790 Z= 0.179 Angle : 0.496 6.681 14403 Z= 0.269 Chirality : 0.037 0.145 1543 Planarity : 0.004 0.038 1752 Dihedral : 19.968 177.982 2064 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.96 % Allowed : 6.17 % Favored : 92.87 % 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: 0.09 (0.25), residues: 1218 helix: 1.23 (0.19), residues: 741 sheet: -0.37 (0.72), residues: 64 loop : -2.08 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 78 HIS 0.005 0.001 HIS C 80 PHE 0.022 0.001 PHE D 242 TYR 0.012 0.001 TYR D 156 ARG 0.003 0.000 ARG D 282 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 ASN cc_start: 0.6094 (t0) cc_final: 0.5645 (t0) outliers start: 10 outliers final: 8 residues processed: 96 average time/residue: 0.5887 time to fit residues: 77.5069 Evaluate side-chains 93 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 341 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 104 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10790 Z= 0.220 Angle : 0.504 6.472 14403 Z= 0.275 Chirality : 0.037 0.154 1543 Planarity : 0.004 0.039 1752 Dihedral : 19.653 178.041 2064 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.96 % Allowed : 7.71 % Favored : 91.33 % 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: 0.10 (0.24), residues: 1218 helix: 1.22 (0.19), residues: 742 sheet: -0.25 (0.72), residues: 64 loop : -2.08 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 78 HIS 0.004 0.001 HIS C 80 PHE 0.017 0.001 PHE D 323 TYR 0.011 0.001 TYR D 156 ARG 0.002 0.000 ARG D 282 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 ASN cc_start: 0.6136 (t0) cc_final: 0.5690 (t0) REVERT: D 257 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.6866 (tt) outliers start: 10 outliers final: 5 residues processed: 93 average time/residue: 0.5506 time to fit residues: 70.5864 Evaluate side-chains 92 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 506 MET Chi-restraints excluded: chain C residue 341 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 59 optimal weight: 20.0000 chunk 104 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10790 Z= 0.335 Angle : 0.561 6.696 14403 Z= 0.306 Chirality : 0.039 0.142 1543 Planarity : 0.004 0.041 1752 Dihedral : 19.888 178.784 2064 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 1.25 % Allowed : 9.15 % Favored : 89.60 % 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: -0.23 (0.24), residues: 1218 helix: 0.94 (0.19), residues: 740 sheet: 0.05 (0.73), residues: 62 loop : -2.24 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 78 HIS 0.006 0.001 HIS C 80 PHE 0.023 0.002 PHE D 323 TYR 0.016 0.002 TYR D 156 ARG 0.004 0.000 ARG D 503 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 ASN cc_start: 0.6157 (t0) cc_final: 0.5724 (t0) REVERT: C 266 PHE cc_start: 0.7304 (t80) cc_final: 0.6974 (m-80) outliers start: 13 outliers final: 8 residues processed: 97 average time/residue: 0.5564 time to fit residues: 75.1398 Evaluate side-chains 94 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 506 MET Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 341 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.4980 chunk 112 optimal weight: 0.3980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 278 ASN C 112 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10790 Z= 0.185 Angle : 0.492 7.549 14403 Z= 0.267 Chirality : 0.037 0.143 1543 Planarity : 0.004 0.042 1752 Dihedral : 19.021 173.877 2064 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.87 % Allowed : 10.21 % Favored : 88.92 % 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: 0.13 (0.24), residues: 1218 helix: 1.27 (0.19), residues: 740 sheet: -0.13 (0.72), residues: 64 loop : -2.13 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 78 HIS 0.003 0.001 HIS C 80 PHE 0.015 0.001 PHE D 323 TYR 0.011 0.001 TYR D 156 ARG 0.003 0.000 ARG D 282 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 1.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 ASN cc_start: 0.6117 (t0) cc_final: 0.5672 (t0) REVERT: C 266 PHE cc_start: 0.7308 (t80) cc_final: 0.7026 (m-80) outliers start: 9 outliers final: 8 residues processed: 92 average time/residue: 0.5885 time to fit residues: 74.7584 Evaluate side-chains 94 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 341 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 313 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10790 Z= 0.293 Angle : 0.538 7.921 14403 Z= 0.293 Chirality : 0.038 0.142 1543 Planarity : 0.004 0.042 1752 Dihedral : 19.202 173.033 2064 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.25 % Allowed : 9.92 % Favored : 88.82 % 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 (0.24), residues: 1218 helix: 1.05 (0.19), residues: 741 sheet: -0.04 (0.72), residues: 64 loop : -2.22 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 78 HIS 0.004 0.001 HIS C 80 PHE 0.021 0.001 PHE D 323 TYR 0.016 0.002 TYR C 19 ARG 0.004 0.000 ARG D 503 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 ASN cc_start: 0.6135 (t0) cc_final: 0.5704 (t0) REVERT: C 266 PHE cc_start: 0.7298 (t80) cc_final: 0.6968 (m-80) outliers start: 13 outliers final: 10 residues processed: 97 average time/residue: 0.5856 time to fit residues: 78.3132 Evaluate side-chains 96 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 341 HIS Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 10790 Z= 0.363 Angle : 0.584 8.074 14403 Z= 0.316 Chirality : 0.040 0.141 1543 Planarity : 0.004 0.042 1752 Dihedral : 19.467 172.740 2064 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 1.35 % Allowed : 10.31 % Favored : 88.34 % 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: -0.38 (0.24), residues: 1218 helix: 0.83 (0.19), residues: 741 sheet: -0.01 (0.73), residues: 64 loop : -2.33 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 78 HIS 0.007 0.001 HIS C 80 PHE 0.029 0.002 PHE D 375 TYR 0.019 0.002 TYR C 19 ARG 0.005 0.001 ARG D 503 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 ASN cc_start: 0.6183 (t0) cc_final: 0.5738 (t0) REVERT: C 266 PHE cc_start: 0.7306 (t80) cc_final: 0.6957 (m-80) outliers start: 14 outliers final: 12 residues processed: 94 average time/residue: 0.5994 time to fit residues: 76.8156 Evaluate side-chains 99 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 508 ILE Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 341 HIS Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10790 Z= 0.234 Angle : 0.521 8.192 14403 Z= 0.283 Chirality : 0.037 0.142 1543 Planarity : 0.004 0.046 1752 Dihedral : 18.846 168.555 2064 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 1.16 % Allowed : 10.50 % Favored : 88.34 % 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: -0.09 (0.24), residues: 1218 helix: 1.09 (0.19), residues: 740 sheet: -0.02 (0.72), residues: 64 loop : -2.25 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 78 HIS 0.004 0.001 HIS C 80 PHE 0.022 0.001 PHE D 375 TYR 0.012 0.001 TYR D 156 ARG 0.003 0.000 ARG D 282 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 ASN cc_start: 0.6144 (t0) cc_final: 0.5705 (t0) REVERT: C 266 PHE cc_start: 0.7331 (t80) cc_final: 0.7016 (m-80) outliers start: 12 outliers final: 11 residues processed: 97 average time/residue: 0.5785 time to fit residues: 76.6986 Evaluate side-chains 99 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 341 HIS Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 chunk 76 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10790 Z= 0.212 Angle : 0.504 7.950 14403 Z= 0.274 Chirality : 0.037 0.140 1543 Planarity : 0.004 0.046 1752 Dihedral : 18.143 172.916 2064 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.06 % Allowed : 11.08 % Favored : 87.86 % 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: 0.09 (0.24), residues: 1218 helix: 1.24 (0.19), residues: 742 sheet: 0.02 (0.72), residues: 64 loop : -2.19 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 78 HIS 0.003 0.001 HIS C 80 PHE 0.018 0.001 PHE D 375 TYR 0.012 0.001 TYR C 19 ARG 0.003 0.000 ARG D 282 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 121 ASN cc_start: 0.6178 (t0) cc_final: 0.5730 (t0) REVERT: C 266 PHE cc_start: 0.7327 (t80) cc_final: 0.7035 (m-80) outliers start: 11 outliers final: 10 residues processed: 97 average time/residue: 0.5982 time to fit residues: 78.9132 Evaluate side-chains 98 residues out of total 1038 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain D residue 427 LEU Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 341 HIS Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 557 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.102558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.076800 restraints weight = 68559.295| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.19 r_work: 0.3344 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10790 Z= 0.196 Angle : 0.497 7.844 14403 Z= 0.269 Chirality : 0.037 0.141 1543 Planarity : 0.004 0.045 1752 Dihedral : 17.444 162.203 2064 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.77 % Allowed : 11.56 % Favored : 87.67 % 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: 0.20 (0.24), residues: 1218 helix: 1.32 (0.19), residues: 743 sheet: -0.02 (0.68), residues: 69 loop : -2.15 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 78 HIS 0.003 0.001 HIS C 80 PHE 0.018 0.001 PHE D 375 TYR 0.012 0.001 TYR C 19 ARG 0.003 0.000 ARG D 282 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4339.56 seconds wall clock time: 77 minutes 47.85 seconds (4667.85 seconds total)