Starting phenix.real_space_refine on Fri Jun 6 11:49:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u64_41943/06_2025/8u64_41943.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u64_41943/06_2025/8u64_41943.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u64_41943/06_2025/8u64_41943.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u64_41943/06_2025/8u64_41943.map" model { file = "/net/cci-nas-00/data/ceres_data/8u64_41943/06_2025/8u64_41943.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u64_41943/06_2025/8u64_41943.cif" } resolution = 3.13 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= 0.015 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: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 4852 2.51 5 N 1331 2.21 5 O 1445 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: 7674 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3772 Classifications: {'peptide': 483} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 456} Chain breaks: 2 Chain: "A" Number of atoms: 3816 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 487, 3802 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 460} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 487, 3802 Classifications: {'peptide': 487} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 460} Chain breaks: 2 bond proxies already assigned to first conformer: 3861 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATRP A 74 " occ=0.37 ... (26 atoms not shown) pdb=" CH2BTRP A 74 " occ=0.63 Time building chain proxies: 8.83, per 1000 atoms: 1.15 Number of scatterers: 7674 At special positions: 0 Unit cell: (121.545, 87.381, 107.091, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 1445 8.00 N 1331 7.00 C 4852 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 1.3 seconds 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1822 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 45.4% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'B' and resid 3 through 15 removed outlier: 3.834A pdb=" N ASN B 15 " --> pdb=" O VAL B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 54 removed outlier: 3.580A pdb=" N VAL B 53 " --> pdb=" O ASN B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 71 through 82 Processing helix chain 'B' and resid 135 through 146 Processing helix chain 'B' and resid 148 through 165 Processing helix chain 'B' and resid 205 through 215 Processing helix chain 'B' and resid 253 through 264 Processing helix chain 'B' and resid 294 through 338 removed outlier: 3.510A pdb=" N GLN B 333 " --> pdb=" O GLN B 329 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET B 338 " --> pdb=" O LEU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 361 removed outlier: 3.750A pdb=" N LEU B 359 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 390 Processing helix chain 'B' and resid 391 through 394 Processing helix chain 'B' and resid 404 through 409 removed outlier: 3.828A pdb=" N VAL B 408 " --> pdb=" O HIS B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 413 removed outlier: 4.437A pdb=" N GLU B 413 " --> pdb=" O PRO B 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 410 through 413' Processing helix chain 'B' and resid 441 through 445 Processing helix chain 'B' and resid 468 through 480 removed outlier: 3.752A pdb=" N GLU B 474 " --> pdb=" O ARG B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 511 removed outlier: 3.748A pdb=" N SER B 501 " --> pdb=" O ASP B 497 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 502 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP B 506 " --> pdb=" O ALA B 502 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU B 507 " --> pdb=" O LEU B 503 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA B 508 " --> pdb=" O GLU B 504 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG B 509 " --> pdb=" O ASN B 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 15 Processing helix chain 'A' and resid 49 through 54 Processing helix chain 'A' and resid 57 through 62 removed outlier: 3.888A pdb=" N ALA A 62 " --> pdb=" O ASP A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.500A pdb=" N ALA A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 146 Processing helix chain 'A' and resid 148 through 165 Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 253 through 264 Processing helix chain 'A' and resid 294 through 336 removed outlier: 3.607A pdb=" N GLN A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 349 Processing helix chain 'A' and resid 352 through 361 removed outlier: 4.183A pdb=" N LEU A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 391 removed outlier: 3.647A pdb=" N ARG A 386 " --> pdb=" O PRO A 382 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 396 removed outlier: 3.754A pdb=" N GLY A 395 " --> pdb=" O TRP A 391 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY A 396 " --> pdb=" O MET A 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 391 through 396' Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.017A pdb=" N VAL A 408 " --> pdb=" O HIS A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 removed outlier: 4.066A pdb=" N VAL A 446 " --> pdb=" O LYS A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 480 removed outlier: 3.578A pdb=" N GLU A 474 " --> pdb=" O ARG A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 514 removed outlier: 4.033A pdb=" N LEU A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 500 " --> pdb=" O ASN A 496 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS A 513 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 27 removed outlier: 6.534A pdb=" N THR B 35 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL B 46 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU B 33 " --> pdb=" O VAL B 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 179 through 187 removed outlier: 7.007A pdb=" N ILE B 171 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLU B 185 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL B 169 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TRP B 280 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LEU B 273 " --> pdb=" O TRP B 280 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU B 282 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL B 271 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N SER B 284 " --> pdb=" O MET B 269 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N MET B 269 " --> pdb=" O SER B 284 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLY B 286 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N SER B 267 " --> pdb=" O GLY B 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 375 through 377 Processing sheet with id=AA4, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA5, first strand: chain 'A' and resid 31 through 36 Processing sheet with id=AA6, first strand: chain 'A' and resid 198 through 199 removed outlier: 5.542A pdb=" N VAL A 182 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG A 173 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA A 184 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TRP A 280 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LEU A 279 " --> pdb=" O GLN A 275 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLN A 275 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 372 through 377 378 hydrogen bonds defined for protein. 1050 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.26 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1424 1.32 - 1.45: 1898 1.45 - 1.57: 4435 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 7835 Sorted by residual: bond pdb=" C GLU A 38 " pdb=" N PRO A 39 " ideal model delta sigma weight residual 1.335 1.350 -0.014 1.30e-02 5.92e+03 1.22e+00 bond pdb=" CA ASP B 344 " pdb=" CB ASP B 344 " ideal model delta sigma weight residual 1.535 1.558 -0.022 2.09e-02 2.29e+03 1.13e+00 bond pdb=" C PRO B 410 " pdb=" N PRO B 411 " ideal model delta sigma weight residual 1.340 1.369 -0.029 2.76e-02 1.31e+03 1.12e+00 bond pdb=" CB PRO B 411 " pdb=" CG PRO B 411 " ideal model delta sigma weight residual 1.492 1.441 0.051 5.00e-02 4.00e+02 1.05e+00 bond pdb=" CB THR B 35 " pdb=" CG2 THR B 35 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.70e-01 ... (remaining 7830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 10481 2.00 - 4.00: 151 4.00 - 5.99: 12 5.99 - 7.99: 5 7.99 - 9.99: 4 Bond angle restraints: 10653 Sorted by residual: angle pdb=" CB MET B 337 " pdb=" CG MET B 337 " pdb=" SD MET B 337 " ideal model delta sigma weight residual 112.70 122.33 -9.63 3.00e+00 1.11e-01 1.03e+01 angle pdb=" CA LEU B 93 " pdb=" CB LEU B 93 " pdb=" CG LEU B 93 " ideal model delta sigma weight residual 116.30 126.29 -9.99 3.50e+00 8.16e-02 8.15e+00 angle pdb=" N PRO A 410 " pdb=" CA PRO A 410 " pdb=" C PRO A 410 " ideal model delta sigma weight residual 110.70 113.78 -3.08 1.22e+00 6.72e-01 6.38e+00 angle pdb=" CA LEU A 66 " pdb=" CB LEU A 66 " pdb=" CG LEU A 66 " ideal model delta sigma weight residual 116.30 124.62 -8.32 3.50e+00 8.16e-02 5.65e+00 angle pdb=" CA LEU A 140 " pdb=" CB LEU A 140 " pdb=" CG LEU A 140 " ideal model delta sigma weight residual 116.30 124.51 -8.21 3.50e+00 8.16e-02 5.50e+00 ... (remaining 10648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 3992 17.23 - 34.47: 532 34.47 - 51.70: 155 51.70 - 68.93: 51 68.93 - 86.17: 15 Dihedral angle restraints: 4745 sinusoidal: 1935 harmonic: 2810 Sorted by residual: dihedral pdb=" CG ARG A 250 " pdb=" CD ARG A 250 " pdb=" NE ARG A 250 " pdb=" CZ ARG A 250 " ideal model delta sinusoidal sigma weight residual 180.00 135.22 44.78 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CA LEU B 423 " pdb=" C LEU B 423 " pdb=" N ALA B 424 " pdb=" CA ALA B 424 " ideal model delta harmonic sigma weight residual -180.00 -164.02 -15.98 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CG ARG B 213 " pdb=" CD ARG B 213 " pdb=" NE ARG B 213 " pdb=" CZ ARG B 213 " ideal model delta sinusoidal sigma weight residual -90.00 -133.68 43.68 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 4742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 650 0.027 - 0.054: 342 0.054 - 0.081: 113 0.081 - 0.108: 62 0.108 - 0.135: 26 Chirality restraints: 1193 Sorted by residual: chirality pdb=" CA ILE B 220 " pdb=" N ILE B 220 " pdb=" C ILE B 220 " pdb=" CB ILE B 220 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA LEU A 140 " pdb=" N LEU A 140 " pdb=" C LEU A 140 " pdb=" CB LEU A 140 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CG LEU A 242 " pdb=" CB LEU A 242 " pdb=" CD1 LEU A 242 " pdb=" CD2 LEU A 242 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 1190 not shown) Planarity restraints: 1386 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 379 " -0.027 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO B 380 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 380 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 380 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 427 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.44e+00 pdb=" N PRO A 428 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 428 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 428 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 235 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO B 236 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.021 5.00e-02 4.00e+02 ... (remaining 1383 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 151 2.68 - 3.23: 7164 3.23 - 3.79: 11869 3.79 - 4.34: 15713 4.34 - 4.90: 26196 Nonbonded interactions: 61093 Sorted by model distance: nonbonded pdb=" OD1 ASN A 224 " pdb=" NZ LYS A 261 " model vdw 2.121 3.120 nonbonded pdb=" O ARG B 386 " pdb=" OG1 THR B 390 " model vdw 2.144 3.040 nonbonded pdb=" O THR A 326 " pdb=" OG1 THR A 330 " model vdw 2.208 3.040 nonbonded pdb=" NE2 HIS B 389 " pdb=" O ASN B 433 " model vdw 2.228 3.120 nonbonded pdb=" OG1 THR B 42 " pdb=" O GLN B 64 " model vdw 2.242 3.040 ... (remaining 61088 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 3 through 73 or resid 75 through 511 or resid 900)) selection = (chain 'B' and (resid 3 through 73 or resid 75 through 511 or resid 900)) } 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=0.37 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: 8.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 25.780 Find NCS groups from input model: 0.350 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 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 : 0.004 0.063 7837 Z= 0.182 Angle : 0.590 9.991 10653 Z= 0.293 Chirality : 0.042 0.135 1193 Planarity : 0.004 0.042 1386 Dihedral : 18.146 86.167 2923 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.48 % Allowed : 27.80 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 (0.28), residues: 961 helix: 0.61 (0.27), residues: 374 sheet: -0.06 (0.43), residues: 156 loop : -0.77 (0.33), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 487 HIS 0.004 0.001 HIS A 30 PHE 0.011 0.001 PHE B 199 TYR 0.019 0.001 TYR A 409 ARG 0.003 0.000 ARG B 168 Details of bonding type rmsd hydrogen bonds : bond 0.22122 ( 378) hydrogen bonds : angle 8.34470 ( 1050) covalent geometry : bond 0.00350 ( 7835) covalent geometry : angle 0.59015 (10653) Misc. bond : bond 0.06325 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 149 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 487 TRP cc_start: 0.6752 (m100) cc_final: 0.6153 (m100) outliers start: 4 outliers final: 3 residues processed: 150 average time/residue: 0.1898 time to fit residues: 38.9290 Evaluate side-chains 150 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 147 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 433 ASN Chi-restraints excluded: chain A residue 345 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.5980 chunk 72 optimal weight: 0.0770 chunk 40 optimal weight: 0.0370 chunk 24 optimal weight: 0.0980 chunk 49 optimal weight: 0.9990 chunk 38 optimal weight: 0.0000 chunk 75 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 overall best weight: 0.1620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.169516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.144554 restraints weight = 27004.105| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 4.10 r_work: 0.3638 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7837 Z= 0.120 Angle : 0.556 8.202 10653 Z= 0.285 Chirality : 0.041 0.137 1193 Planarity : 0.005 0.041 1386 Dihedral : 6.837 72.702 1092 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.77 % Allowed : 24.79 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.04 (0.28), residues: 961 helix: 1.03 (0.25), residues: 387 sheet: -0.10 (0.43), residues: 157 loop : -0.82 (0.33), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.004 0.001 HIS A 287 PHE 0.010 0.001 PHE A 438 TYR 0.010 0.001 TYR A 409 ARG 0.003 0.000 ARG B 168 Details of bonding type rmsd hydrogen bonds : bond 0.04112 ( 378) hydrogen bonds : angle 5.81130 ( 1050) covalent geometry : bond 0.00266 ( 7835) covalent geometry : angle 0.55572 (10653) Misc. bond : bond 0.00035 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLN cc_start: 0.7672 (mp10) cc_final: 0.7414 (mp10) REVERT: B 325 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6971 (mp0) REVERT: B 337 MET cc_start: 0.7024 (tpp) cc_final: 0.6653 (tpp) REVERT: B 487 TRP cc_start: 0.7016 (m100) cc_final: 0.6313 (m100) REVERT: A 319 GLU cc_start: 0.7025 (tm-30) cc_final: 0.6824 (tm-30) REVERT: A 391 TRP cc_start: 0.7995 (OUTLIER) cc_final: 0.6858 (t60) outliers start: 23 outliers final: 11 residues processed: 165 average time/residue: 0.1809 time to fit residues: 41.0501 Evaluate side-chains 163 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 391 TRP Chi-restraints excluded: chain A residue 514 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 47 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 42 optimal weight: 0.2980 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN ** B 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.162207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.142068 restraints weight = 11833.675| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.33 r_work: 0.3716 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3718 r_free = 0.3718 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3718 r_free = 0.3718 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 7837 Z= 0.225 Angle : 0.614 8.210 10653 Z= 0.314 Chirality : 0.044 0.143 1193 Planarity : 0.005 0.051 1386 Dihedral : 6.989 70.149 1088 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.01 % Favored : 94.89 % Rotamer: Outliers : 3.85 % Allowed : 23.83 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.01 (0.28), residues: 961 helix: 1.09 (0.25), residues: 379 sheet: -0.21 (0.43), residues: 154 loop : -0.89 (0.33), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 487 HIS 0.006 0.001 HIS A 30 PHE 0.014 0.002 PHE A 493 TYR 0.011 0.002 TYR A 400 ARG 0.003 0.000 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.04296 ( 378) hydrogen bonds : angle 5.76683 ( 1050) covalent geometry : bond 0.00518 ( 7835) covalent geometry : angle 0.61442 (10653) Misc. bond : bond 0.00034 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 143 LEU cc_start: 0.8389 (mt) cc_final: 0.8174 (mp) REVERT: B 325 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6936 (mp0) REVERT: B 337 MET cc_start: 0.6795 (tpp) cc_final: 0.6254 (tpp) REVERT: B 388 LEU cc_start: 0.4157 (OUTLIER) cc_final: 0.3910 (tp) REVERT: B 487 TRP cc_start: 0.6829 (m100) cc_final: 0.6177 (m100) REVERT: A 391 TRP cc_start: 0.8009 (OUTLIER) cc_final: 0.6560 (t60) outliers start: 32 outliers final: 20 residues processed: 173 average time/residue: 0.1733 time to fit residues: 41.8518 Evaluate side-chains 174 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 391 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 74 optimal weight: 0.9980 chunk 33 optimal weight: 0.0970 chunk 61 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 79 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN ** B 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN A 323 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.166460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.142351 restraints weight = 26661.071| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 3.80 r_work: 0.3611 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7837 Z= 0.185 Angle : 0.596 8.244 10653 Z= 0.305 Chirality : 0.043 0.195 1193 Planarity : 0.005 0.054 1386 Dihedral : 6.906 78.009 1088 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.97 % Allowed : 25.15 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.00 (0.28), residues: 961 helix: 1.17 (0.25), residues: 379 sheet: -0.27 (0.43), residues: 149 loop : -0.92 (0.32), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 487 HIS 0.005 0.001 HIS B 30 PHE 0.013 0.002 PHE A 493 TYR 0.010 0.001 TYR A 172 ARG 0.003 0.000 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.03872 ( 378) hydrogen bonds : angle 5.64062 ( 1050) covalent geometry : bond 0.00425 ( 7835) covalent geometry : angle 0.59629 (10653) Misc. bond : bond 0.00033 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLN cc_start: 0.7628 (mp10) cc_final: 0.7394 (mp10) REVERT: B 337 MET cc_start: 0.7078 (tpp) cc_final: 0.6412 (tpp) REVERT: B 487 TRP cc_start: 0.7083 (m100) cc_final: 0.6381 (m100) outliers start: 33 outliers final: 23 residues processed: 175 average time/residue: 0.1767 time to fit residues: 43.3393 Evaluate side-chains 176 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 514 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 90 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 91 optimal weight: 0.4980 chunk 58 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN ** B 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.161760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.137875 restraints weight = 22543.781| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 3.55 r_work: 0.3614 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3617 r_free = 0.3617 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 7837 Z= 0.218 Angle : 0.632 9.223 10653 Z= 0.318 Chirality : 0.044 0.179 1193 Planarity : 0.005 0.058 1386 Dihedral : 6.938 70.383 1088 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.33 % Allowed : 24.55 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 (0.28), residues: 961 helix: 1.08 (0.25), residues: 379 sheet: -0.30 (0.43), residues: 149 loop : -0.97 (0.32), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 487 HIS 0.005 0.001 HIS B 30 PHE 0.013 0.002 PHE A 493 TYR 0.017 0.002 TYR A 409 ARG 0.003 0.000 ARG B 168 Details of bonding type rmsd hydrogen bonds : bond 0.03993 ( 378) hydrogen bonds : angle 5.69862 ( 1050) covalent geometry : bond 0.00503 ( 7835) covalent geometry : angle 0.63181 (10653) Misc. bond : bond 0.00033 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 337 MET cc_start: 0.7104 (tpp) cc_final: 0.6380 (tpp) REVERT: B 487 TRP cc_start: 0.7061 (m100) cc_final: 0.6467 (m100) REVERT: A 505 ASN cc_start: 0.7940 (t0) cc_final: 0.7582 (t0) outliers start: 35 outliers final: 27 residues processed: 173 average time/residue: 0.2907 time to fit residues: 71.5328 Evaluate side-chains 179 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 139 MET Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 360 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.1980 chunk 93 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 43 optimal weight: 0.2980 chunk 63 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 33 optimal weight: 0.0980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN ** B 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.163754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.140353 restraints weight = 24037.363| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 3.53 r_work: 0.3646 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3648 r_free = 0.3648 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3648 r_free = 0.3648 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7837 Z= 0.138 Angle : 0.580 9.481 10653 Z= 0.291 Chirality : 0.042 0.179 1193 Planarity : 0.005 0.057 1386 Dihedral : 6.735 66.551 1088 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.85 % Allowed : 24.79 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.28), residues: 961 helix: 1.26 (0.25), residues: 385 sheet: -0.22 (0.44), residues: 149 loop : -0.87 (0.33), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 391 HIS 0.004 0.001 HIS A 30 PHE 0.012 0.002 PHE A 493 TYR 0.008 0.001 TYR A 172 ARG 0.003 0.000 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.03340 ( 378) hydrogen bonds : angle 5.38079 ( 1050) covalent geometry : bond 0.00320 ( 7835) covalent geometry : angle 0.58016 (10653) Misc. bond : bond 0.00030 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLN cc_start: 0.7579 (mp10) cc_final: 0.7317 (mp10) REVERT: B 337 MET cc_start: 0.7081 (tpp) cc_final: 0.6454 (tpp) REVERT: B 487 TRP cc_start: 0.7019 (m100) cc_final: 0.6206 (m100) REVERT: A 505 ASN cc_start: 0.7871 (t0) cc_final: 0.7487 (t0) outliers start: 31 outliers final: 25 residues processed: 176 average time/residue: 0.1860 time to fit residues: 45.6632 Evaluate side-chains 181 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 510 GLN Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 514 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 47 optimal weight: 0.0980 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 0.0070 chunk 65 optimal weight: 0.0030 chunk 36 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.1408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN B 352 GLN A 142 GLN A 215 ASN A 306 GLN ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.170265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.146194 restraints weight = 23017.916| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 3.74 r_work: 0.3676 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3674 r_free = 0.3674 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3674 r_free = 0.3674 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7837 Z= 0.105 Angle : 0.566 10.187 10653 Z= 0.279 Chirality : 0.041 0.174 1193 Planarity : 0.005 0.055 1386 Dihedral : 6.880 88.520 1088 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.89 % Allowed : 25.99 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.28), residues: 961 helix: 1.54 (0.26), residues: 385 sheet: -0.18 (0.41), residues: 157 loop : -0.73 (0.33), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 476 HIS 0.003 0.001 HIS A 389 PHE 0.012 0.001 PHE B 199 TYR 0.020 0.001 TYR A 409 ARG 0.002 0.000 ARG A 209 Details of bonding type rmsd hydrogen bonds : bond 0.02930 ( 378) hydrogen bonds : angle 5.04913 ( 1050) covalent geometry : bond 0.00240 ( 7835) covalent geometry : angle 0.56571 (10653) Misc. bond : bond 0.00024 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLN cc_start: 0.7520 (mp10) cc_final: 0.7279 (mp10) REVERT: B 142 GLN cc_start: 0.8064 (mm110) cc_final: 0.7809 (mt0) REVERT: B 337 MET cc_start: 0.7060 (tpp) cc_final: 0.6471 (tpp) REVERT: B 487 TRP cc_start: 0.6991 (m100) cc_final: 0.6165 (m100) REVERT: A 337 MET cc_start: 0.7195 (ttt) cc_final: 0.6965 (tpp) REVERT: A 505 ASN cc_start: 0.7806 (t0) cc_final: 0.7408 (t0) outliers start: 23 outliers final: 19 residues processed: 165 average time/residue: 0.1792 time to fit residues: 41.1757 Evaluate side-chains 168 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 510 GLN Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 514 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 62 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 0.0870 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 87 optimal weight: 0.0570 chunk 74 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN ** B 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.163738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.140531 restraints weight = 19959.168| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 3.34 r_work: 0.3661 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3663 r_free = 0.3663 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3663 r_free = 0.3663 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7837 Z= 0.159 Angle : 0.613 10.684 10653 Z= 0.302 Chirality : 0.043 0.171 1193 Planarity : 0.005 0.056 1386 Dihedral : 6.790 83.299 1088 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.13 % Allowed : 25.87 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.35 (0.28), residues: 961 helix: 1.48 (0.25), residues: 385 sheet: -0.10 (0.42), residues: 154 loop : -0.79 (0.33), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 448 HIS 0.004 0.001 HIS A 30 PHE 0.012 0.002 PHE A 493 TYR 0.012 0.001 TYR A 409 ARG 0.002 0.000 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.03302 ( 378) hydrogen bonds : angle 5.19594 ( 1050) covalent geometry : bond 0.00372 ( 7835) covalent geometry : angle 0.61263 (10653) Misc. bond : bond 0.00028 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLN cc_start: 0.7577 (mp10) cc_final: 0.7326 (mp10) REVERT: B 142 GLN cc_start: 0.8057 (mm110) cc_final: 0.7802 (mt0) REVERT: B 337 MET cc_start: 0.7048 (tpp) cc_final: 0.6473 (tpp) REVERT: B 487 TRP cc_start: 0.7016 (m100) cc_final: 0.6168 (m100) REVERT: A 505 ASN cc_start: 0.7834 (t0) cc_final: 0.7476 (t0) outliers start: 25 outliers final: 23 residues processed: 164 average time/residue: 0.1709 time to fit residues: 39.2315 Evaluate side-chains 172 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 514 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 62 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 89 optimal weight: 0.3980 chunk 83 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 0.3980 chunk 57 optimal weight: 0.3980 chunk 78 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN B 352 GLN B 389 HIS A 306 GLN ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.167081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.142030 restraints weight = 30932.102| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 4.53 r_work: 0.3575 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7837 Z= 0.175 Angle : 0.618 10.221 10653 Z= 0.307 Chirality : 0.043 0.172 1193 Planarity : 0.005 0.056 1386 Dihedral : 6.729 75.835 1088 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.37 % Allowed : 25.51 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 (0.28), residues: 961 helix: 1.35 (0.25), residues: 385 sheet: -0.11 (0.43), residues: 149 loop : -0.85 (0.33), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 448 HIS 0.005 0.001 HIS B 389 PHE 0.012 0.002 PHE A 493 TYR 0.010 0.001 TYR A 172 ARG 0.003 0.000 ARG B 509 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 378) hydrogen bonds : angle 5.30335 ( 1050) covalent geometry : bond 0.00406 ( 7835) covalent geometry : angle 0.61806 (10653) Misc. bond : bond 0.00029 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 GLN cc_start: 0.8128 (mm110) cc_final: 0.7831 (mt0) REVERT: B 337 MET cc_start: 0.7246 (tpp) cc_final: 0.6564 (tpp) REVERT: B 487 TRP cc_start: 0.7134 (m100) cc_final: 0.6264 (m100) REVERT: A 505 ASN cc_start: 0.7920 (t0) cc_final: 0.7571 (t0) outliers start: 27 outliers final: 25 residues processed: 170 average time/residue: 0.1777 time to fit residues: 41.8967 Evaluate side-chains 173 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 360 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 12 optimal weight: 0.6980 chunk 70 optimal weight: 0.4980 chunk 19 optimal weight: 0.3980 chunk 52 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 71 optimal weight: 0.0970 chunk 68 optimal weight: 0.3980 chunk 67 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.167742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.146660 restraints weight = 13588.863| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.64 r_work: 0.3712 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3711 r_free = 0.3711 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3711 r_free = 0.3711 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7837 Z= 0.149 Angle : 0.611 10.423 10653 Z= 0.302 Chirality : 0.043 0.174 1193 Planarity : 0.005 0.056 1386 Dihedral : 6.794 72.587 1088 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.25 % Allowed : 25.75 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.28 (0.28), residues: 961 helix: 1.43 (0.25), residues: 383 sheet: -0.08 (0.43), residues: 143 loop : -0.83 (0.32), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 448 HIS 0.005 0.001 HIS B 389 PHE 0.012 0.002 PHE A 493 TYR 0.011 0.001 TYR A 409 ARG 0.005 0.000 ARG B 288 Details of bonding type rmsd hydrogen bonds : bond 0.03282 ( 378) hydrogen bonds : angle 5.23150 ( 1050) covalent geometry : bond 0.00349 ( 7835) covalent geometry : angle 0.61107 (10653) Misc. bond : bond 0.00029 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLN cc_start: 0.7534 (mp10) cc_final: 0.7315 (mp10) REVERT: B 142 GLN cc_start: 0.8047 (mm110) cc_final: 0.7787 (mt0) REVERT: B 337 MET cc_start: 0.6982 (tpp) cc_final: 0.6442 (tpp) REVERT: B 487 TRP cc_start: 0.6904 (m100) cc_final: 0.6031 (m100) REVERT: A 505 ASN cc_start: 0.7738 (t0) cc_final: 0.7390 (t0) outliers start: 26 outliers final: 24 residues processed: 160 average time/residue: 0.1785 time to fit residues: 39.5682 Evaluate side-chains 168 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 335 HIS Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 381 GLU Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 360 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 66 optimal weight: 0.3980 chunk 5 optimal weight: 0.5980 chunk 70 optimal weight: 0.4980 chunk 13 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 27 optimal weight: 0.0270 chunk 21 optimal weight: 0.0000 chunk 67 optimal weight: 0.0060 chunk 19 optimal weight: 0.0870 overall best weight: 0.1036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN B 351 GLN B 352 GLN ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.171181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.147075 restraints weight = 23475.677| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 3.80 r_work: 0.3683 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7837 Z= 0.103 Angle : 0.574 11.064 10653 Z= 0.283 Chirality : 0.041 0.171 1193 Planarity : 0.005 0.057 1386 Dihedral : 6.603 69.092 1088 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.65 % Allowed : 26.23 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.54 (0.28), residues: 961 helix: 1.63 (0.26), residues: 388 sheet: -0.06 (0.42), residues: 151 loop : -0.66 (0.33), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 448 HIS 0.004 0.001 HIS B 389 PHE 0.009 0.001 PHE A 493 TYR 0.014 0.001 TYR A 409 ARG 0.004 0.000 ARG B 288 Details of bonding type rmsd hydrogen bonds : bond 0.02870 ( 378) hydrogen bonds : angle 4.93519 ( 1050) covalent geometry : bond 0.00239 ( 7835) covalent geometry : angle 0.57367 (10653) Misc. bond : bond 0.00031 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5591.78 seconds wall clock time: 97 minutes 53.78 seconds (5873.78 seconds total)