Starting phenix.real_space_refine on Fri Aug 22 20:27:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u64_41943/08_2025/8u64_41943.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u64_41943/08_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_41943/08_2025/8u64_41943.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u64_41943/08_2025/8u64_41943.map" model { file = "/net/cci-nas-00/data/ceres_data/8u64_41943/08_2025/8u64_41943.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u64_41943/08_2025/8u64_41943.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.41, per 1000 atoms: 0.31 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: 0.52 Conformation dependent library (CDL) restraints added in 398.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.21 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: 0.98 Time building geometry restraints manager: 0.69 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 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: 11.920 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.810 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.290 ------------------------------------------------------------------------------- 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 : 11.13 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG B 168 TYR 0.019 0.001 TYR A 409 PHE 0.011 0.001 PHE B 199 TRP 0.013 0.001 TRP A 487 HIS 0.004 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 7835) covalent geometry : angle 0.59015 (10653) hydrogen bonds : bond 0.22122 ( 378) hydrogen bonds : angle 8.34470 ( 1050) 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 : 0.252 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: 0.0729 time to fit residues: 15.1909 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 : 0.277 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.0270 chunk 33 optimal weight: 0.0370 chunk 65 optimal weight: 0.0980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.0980 chunk 74 optimal weight: 0.9990 overall best weight: 0.1716 ------------------------------------------------------------------------------- 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 352 GLN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.169335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.144614 restraints weight = 25981.782| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 4.01 r_work: 0.3644 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.1073 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= 0.119 Angle : 0.557 8.140 10653 Z= 0.285 Chirality : 0.042 0.136 1193 Planarity : 0.005 0.041 1386 Dihedral : 6.838 72.744 1092 Min Nonbonded Distance : 2.543 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG B 168 TYR 0.010 0.001 TYR A 409 PHE 0.009 0.001 PHE A 493 TRP 0.008 0.001 TRP A 476 HIS 0.004 0.001 HIS A 389 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 7835) covalent geometry : angle 0.55697 (10653) hydrogen bonds : bond 0.04042 ( 378) hydrogen bonds : angle 5.79368 ( 1050) Misc. bond : bond 0.00033 ( 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 : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLN cc_start: 0.7664 (mp10) cc_final: 0.7405 (mp10) REVERT: B 325 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: B 337 MET cc_start: 0.6991 (tpp) cc_final: 0.6629 (tpp) REVERT: B 487 TRP cc_start: 0.7011 (m100) cc_final: 0.6304 (m100) outliers start: 23 outliers final: 12 residues processed: 165 average time/residue: 0.0857 time to fit residues: 19.4307 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 : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 228 VAL 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 514 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 61 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 0.2980 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 66 optimal weight: 0.3980 chunk 27 optimal weight: 0.0970 chunk 87 optimal weight: 0.0980 overall best weight: 0.3178 ------------------------------------------------------------------------------- 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 = 0.4132 r_free = 0.4132 target = 0.168615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.145331 restraints weight = 19887.856| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 3.38 r_work: 0.3668 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3669 r_free = 0.3669 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3669 r_free = 0.3669 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7837 Z= 0.138 Angle : 0.552 8.023 10653 Z= 0.282 Chirality : 0.042 0.136 1193 Planarity : 0.005 0.047 1386 Dihedral : 6.724 68.201 1088 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.25 % Allowed : 24.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.28), residues: 961 helix: 1.24 (0.25), residues: 387 sheet: -0.18 (0.42), residues: 157 loop : -0.82 (0.33), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 214 TYR 0.009 0.001 TYR A 409 PHE 0.013 0.001 PHE A 493 TRP 0.008 0.001 TRP A 487 HIS 0.004 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 7835) covalent geometry : angle 0.55185 (10653) hydrogen bonds : bond 0.03706 ( 378) hydrogen bonds : angle 5.44845 ( 1050) Misc. bond : bond 0.00028 ( 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 176 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLN cc_start: 0.7626 (mp10) cc_final: 0.7339 (mp10) REVERT: B 143 LEU cc_start: 0.8289 (mt) cc_final: 0.8085 (mp) REVERT: B 337 MET cc_start: 0.6920 (tpp) cc_final: 0.6372 (tpp) REVERT: B 487 TRP cc_start: 0.6968 (m100) cc_final: 0.6225 (m100) outliers start: 27 outliers final: 16 residues processed: 166 average time/residue: 0.0808 time to fit residues: 18.9681 Evaluate side-chains 166 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 159 GLU Chi-restraints excluded: chain B residue 248 THR 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 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 514 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 81 optimal weight: 0.0970 chunk 94 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 0.0370 chunk 2 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 overall best weight: 0.3856 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.164261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.141171 restraints weight = 19680.390| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 3.31 r_work: 0.3668 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3669 r_free = 0.3669 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3669 r_free = 0.3669 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7837 Z= 0.152 Angle : 0.577 10.751 10653 Z= 0.290 Chirality : 0.042 0.137 1193 Planarity : 0.005 0.051 1386 Dihedral : 6.801 85.417 1088 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.61 % Allowed : 24.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.28), residues: 961 helix: 1.33 (0.26), residues: 385 sheet: -0.15 (0.42), residues: 154 loop : -0.83 (0.33), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 214 TYR 0.008 0.001 TYR A 172 PHE 0.012 0.002 PHE A 493 TRP 0.009 0.001 TRP A 487 HIS 0.004 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 7835) covalent geometry : angle 0.57666 (10653) hydrogen bonds : bond 0.03598 ( 378) hydrogen bonds : angle 5.39443 ( 1050) Misc. bond : bond 0.00029 ( 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 184 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 337 MET cc_start: 0.6986 (tpp) cc_final: 0.6364 (tpp) REVERT: B 487 TRP cc_start: 0.6937 (m100) cc_final: 0.6158 (m100) outliers start: 30 outliers final: 22 residues processed: 172 average time/residue: 0.0815 time to fit residues: 19.6018 Evaluate side-chains 170 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.167 ------------------------------------------------------------------------------- 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 159 GLU 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 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 360 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 12 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 142 GLN A 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.161360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.137866 restraints weight = 20986.494| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 3.38 r_work: 0.3618 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- 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 = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 7837 Z= 0.251 Angle : 0.658 9.324 10653 Z= 0.330 Chirality : 0.045 0.148 1193 Planarity : 0.005 0.056 1386 Dihedral : 6.989 77.745 1088 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.97 % Allowed : 25.51 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.28), residues: 961 helix: 1.11 (0.26), residues: 379 sheet: -0.34 (0.42), residues: 160 loop : -0.90 (0.33), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 439 TYR 0.016 0.002 TYR A 409 PHE 0.014 0.002 PHE A 438 TRP 0.017 0.002 TRP B 487 HIS 0.006 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00580 ( 7835) covalent geometry : angle 0.65795 (10653) hydrogen bonds : bond 0.04145 ( 378) hydrogen bonds : angle 5.67531 ( 1050) Misc. bond : bond 0.00031 ( 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 189 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 337 MET cc_start: 0.7099 (tpp) cc_final: 0.6393 (tpp) REVERT: B 487 TRP cc_start: 0.7017 (m100) cc_final: 0.6433 (m100) REVERT: A 505 ASN cc_start: 0.8009 (t0) cc_final: 0.7661 (t0) outliers start: 33 outliers final: 25 residues processed: 175 average time/residue: 0.0781 time to fit residues: 19.1143 Evaluate side-chains 178 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 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 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 478 VAL Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 95 MET 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 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 91 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 65 optimal weight: 0.3980 chunk 81 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 142 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 = 0.4080 r_free = 0.4080 target = 0.162365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.139040 restraints weight = 21162.046| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 3.42 r_work: 0.3631 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7837 Z= 0.192 Angle : 0.633 9.371 10653 Z= 0.314 Chirality : 0.044 0.189 1193 Planarity : 0.005 0.058 1386 Dihedral : 6.909 66.120 1088 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.85 % Allowed : 25.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.28), residues: 961 helix: 1.15 (0.25), residues: 379 sheet: -0.37 (0.42), residues: 156 loop : -0.92 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 168 TYR 0.010 0.001 TYR A 172 PHE 0.012 0.002 PHE A 493 TRP 0.011 0.002 TRP B 487 HIS 0.005 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 7835) covalent geometry : angle 0.63263 (10653) hydrogen bonds : bond 0.03778 ( 378) hydrogen bonds : angle 5.57281 ( 1050) Misc. bond : bond 0.00032 ( 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 184 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLN cc_start: 0.7574 (mp10) cc_final: 0.7304 (mp10) REVERT: B 337 MET cc_start: 0.7094 (tpp) cc_final: 0.6445 (tpp) REVERT: B 487 TRP cc_start: 0.7020 (m100) cc_final: 0.6244 (m100) REVERT: A 505 ASN cc_start: 0.7976 (t0) cc_final: 0.7618 (t0) outliers start: 31 outliers final: 25 residues processed: 168 average time/residue: 0.0726 time to fit residues: 17.4021 Evaluate side-chains 180 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.200 ------------------------------------------------------------------------------- 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 159 GLU 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 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 217 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 360 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 21 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 19 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 33 optimal weight: 0.4980 chunk 78 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4080 r_free = 0.4080 target = 0.162251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.142536 restraints weight = 11526.294| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.30 r_work: 0.3719 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3723 r_free = 0.3723 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3723 r_free = 0.3723 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7837 Z= 0.197 Angle : 0.637 9.889 10653 Z= 0.315 Chirality : 0.044 0.184 1193 Planarity : 0.005 0.059 1386 Dihedral : 6.956 65.943 1088 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.33 % Allowed : 24.43 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.28), residues: 961 helix: 1.19 (0.25), residues: 380 sheet: -0.34 (0.43), residues: 155 loop : -0.94 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 288 TYR 0.017 0.002 TYR A 409 PHE 0.012 0.002 PHE A 493 TRP 0.011 0.002 TRP B 487 HIS 0.005 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 7835) covalent geometry : angle 0.63691 (10653) hydrogen bonds : bond 0.03692 ( 378) hydrogen bonds : angle 5.51264 ( 1050) Misc. bond : bond 0.00032 ( 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 191 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 337 MET cc_start: 0.6898 (tpp) cc_final: 0.6309 (tpp) REVERT: B 487 TRP cc_start: 0.6885 (m100) cc_final: 0.6207 (m100) REVERT: A 505 ASN cc_start: 0.7854 (t0) cc_final: 0.7497 (t0) outliers start: 35 outliers final: 29 residues processed: 174 average time/residue: 0.0742 time to fit residues: 18.1226 Evaluate side-chains 186 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 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 478 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 510 GLN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 93 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 84 optimal weight: 0.2980 chunk 62 optimal weight: 0.5980 chunk 24 optimal weight: 0.2980 chunk 91 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 0.0570 chunk 17 optimal weight: 0.9980 overall best weight: 0.3698 ------------------------------------------------------------------------------- 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 142 GLN A 306 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 = 0.4089 r_free = 0.4089 target = 0.163231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.139751 restraints weight = 25358.433| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 3.91 r_work: 0.3632 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7837 Z= 0.151 Angle : 0.610 9.946 10653 Z= 0.300 Chirality : 0.042 0.180 1193 Planarity : 0.005 0.058 1386 Dihedral : 6.944 73.295 1088 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.28), residues: 961 helix: 1.32 (0.25), residues: 386 sheet: -0.28 (0.43), residues: 156 loop : -0.91 (0.33), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 168 TYR 0.008 0.001 TYR A 172 PHE 0.011 0.001 PHE B 199 TRP 0.009 0.001 TRP B 391 HIS 0.004 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 7835) covalent geometry : angle 0.60982 (10653) hydrogen bonds : bond 0.03397 ( 378) hydrogen bonds : angle 5.35417 ( 1050) Misc. bond : bond 0.00030 ( 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 183 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLN cc_start: 0.7547 (mp10) cc_final: 0.7279 (mp10) REVERT: B 337 MET cc_start: 0.7119 (tpp) cc_final: 0.6491 (tpp) REVERT: B 487 TRP cc_start: 0.7038 (m100) cc_final: 0.6273 (m100) REVERT: A 505 ASN cc_start: 0.7902 (t0) cc_final: 0.7529 (t0) outliers start: 26 outliers final: 23 residues processed: 168 average time/residue: 0.0709 time to fit residues: 16.7442 Evaluate side-chains 175 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 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 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 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 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 80 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 86 optimal weight: 0.0030 chunk 62 optimal weight: 0.6980 chunk 41 optimal weight: 0.0670 chunk 79 optimal weight: 0.9990 overall best weight: 0.4528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 ASN B 306 GLN B 352 GLN 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 = 0.4087 r_free = 0.4087 target = 0.162908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.139557 restraints weight = 21059.458| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 3.41 r_work: 0.3633 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3642 r_free = 0.3642 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3642 r_free = 0.3642 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.1768 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= 0.170 Angle : 0.632 10.548 10653 Z= 0.311 Chirality : 0.043 0.180 1193 Planarity : 0.005 0.058 1386 Dihedral : 6.873 68.363 1088 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.61 % Allowed : 25.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.28), residues: 961 helix: 1.28 (0.25), residues: 386 sheet: -0.27 (0.42), residues: 156 loop : -0.91 (0.33), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 214 TYR 0.019 0.001 TYR A 409 PHE 0.012 0.002 PHE A 493 TRP 0.010 0.002 TRP B 487 HIS 0.004 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 7835) covalent geometry : angle 0.63164 (10653) hydrogen bonds : bond 0.03452 ( 378) hydrogen bonds : angle 5.35108 ( 1050) 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 187 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLN cc_start: 0.7564 (mp10) cc_final: 0.7290 (mp10) REVERT: B 337 MET cc_start: 0.7052 (tpp) cc_final: 0.6428 (tpp) REVERT: B 487 TRP cc_start: 0.7032 (m100) cc_final: 0.6271 (m100) REVERT: A 337 MET cc_start: 0.7287 (ttt) cc_final: 0.7062 (tpp) REVERT: A 505 ASN cc_start: 0.7905 (t0) cc_final: 0.7567 (t0) outliers start: 29 outliers final: 26 residues processed: 171 average time/residue: 0.0745 time to fit residues: 17.8283 Evaluate side-chains 182 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 215 ASN 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 478 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 28 optimal weight: 1.9990 chunk 88 optimal weight: 0.0170 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 0.3980 chunk 36 optimal weight: 0.2980 chunk 62 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.162363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.139410 restraints weight = 19930.216| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 3.32 r_work: 0.3642 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3641 r_free = 0.3641 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3641 r_free = 0.3641 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7837 Z= 0.174 Angle : 0.632 10.805 10653 Z= 0.311 Chirality : 0.043 0.179 1193 Planarity : 0.005 0.058 1386 Dihedral : 6.871 67.806 1088 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.61 % Allowed : 25.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.28), residues: 961 helix: 1.25 (0.25), residues: 386 sheet: -0.24 (0.42), residues: 155 loop : -0.93 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.011 0.001 TYR A 409 PHE 0.012 0.002 PHE A 493 TRP 0.014 0.002 TRP B 448 HIS 0.004 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 7835) covalent geometry : angle 0.63170 (10653) hydrogen bonds : bond 0.03493 ( 378) hydrogen bonds : angle 5.34563 ( 1050) Misc. bond : bond 0.00030 ( 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 186 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLN cc_start: 0.7550 (mp10) cc_final: 0.7260 (mp10) REVERT: B 337 MET cc_start: 0.7024 (tpp) cc_final: 0.6411 (tpp) REVERT: B 487 TRP cc_start: 0.7016 (m100) cc_final: 0.6249 (m100) REVERT: A 337 MET cc_start: 0.7282 (ttt) cc_final: 0.7057 (tpp) REVERT: A 505 ASN cc_start: 0.7893 (t0) cc_final: 0.7541 (t0) outliers start: 29 outliers final: 27 residues processed: 171 average time/residue: 0.0761 time to fit residues: 18.2842 Evaluate side-chains 175 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 215 ASN 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 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 478 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 2 optimal weight: 0.9990 chunk 44 optimal weight: 0.0970 chunk 68 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 45 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 95 optimal weight: 0.3980 chunk 77 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 GLN B 351 GLN B 352 GLN 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 = 0.4088 r_free = 0.4088 target = 0.162981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.141319 restraints weight = 16227.311| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.89 r_work: 0.3680 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7837 Z= 0.155 Angle : 0.626 10.403 10653 Z= 0.309 Chirality : 0.043 0.179 1193 Planarity : 0.005 0.060 1386 Dihedral : 6.907 73.780 1088 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.28), residues: 961 helix: 1.30 (0.25), residues: 384 sheet: -0.18 (0.43), residues: 149 loop : -0.93 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.021 0.001 TYR A 409 PHE 0.011 0.002 PHE A 493 TRP 0.017 0.002 TRP B 448 HIS 0.004 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 7835) covalent geometry : angle 0.62628 (10653) hydrogen bonds : bond 0.03395 ( 378) hydrogen bonds : angle 5.31846 ( 1050) Misc. bond : bond 0.00030 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2336.47 seconds wall clock time: 40 minutes 40.21 seconds (2440.21 seconds total)