Starting phenix.real_space_refine on Sun May 11 07:09:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u64_41943/05_2025/8u64_41943.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u64_41943/05_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_41943/05_2025/8u64_41943.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u64_41943/05_2025/8u64_41943.map" model { file = "/net/cci-nas-00/data/ceres_data/8u64_41943/05_2025/8u64_41943.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u64_41943/05_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-5687/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: 8.73, per 1000 atoms: 1.14 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: 2.15 Conformation dependent library (CDL) restraints added in 1.4 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: 0.77 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: 2.18 Time building geometry restraints manager: 2.47 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: 12.520 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.300 Find NCS groups from input model: 0.350 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.520 ------------------------------------------------------------------------------- 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 : 0.799 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: 0.1926 time to fit residues: 39.8114 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 : 0.753 ------------------------------------------------------------------------------- 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 = 0.169515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.144564 restraints weight = 27004.159| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 4.10 r_work: 0.3639 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- 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 = 0.37 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 = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 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 5.81131 ( 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 : 0.860 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: 0.7225 (OUTLIER) cc_final: 0.6974 (mp0) REVERT: B 337 MET cc_start: 0.7025 (tpp) cc_final: 0.6652 (tpp) REVERT: B 487 TRP cc_start: 0.7016 (m100) cc_final: 0.6312 (m100) REVERT: A 319 GLU cc_start: 0.7026 (tm-30) cc_final: 0.6824 (tm-30) REVERT: A 391 TRP cc_start: 0.7994 (OUTLIER) cc_final: 0.6857 (t60) outliers start: 23 outliers final: 11 residues processed: 165 average time/residue: 0.1857 time to fit residues: 42.1349 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 : 0.734 ------------------------------------------------------------------------------- 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: 0.9980 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 42 optimal weight: 0.2980 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4073 r_free = 0.4073 target = 0.161617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.141520 restraints weight = 11751.467| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.32 r_work: 0.3705 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 7837 Z= 0.252 Angle : 0.637 8.195 10653 Z= 0.326 Chirality : 0.045 0.148 1193 Planarity : 0.005 0.052 1386 Dihedral : 7.071 70.150 1088 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.22 % Favored : 94.68 % Rotamer: Outliers : 3.97 % Allowed : 23.83 % Favored : 72.20 % 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: 1.00 (0.25), residues: 379 sheet: -0.23 (0.43), residues: 155 loop : -0.91 (0.33), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 487 HIS 0.006 0.001 HIS A 30 PHE 0.014 0.002 PHE A 493 TYR 0.012 0.002 TYR A 400 ARG 0.003 0.000 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.04483 ( 378) hydrogen bonds : angle 5.85488 ( 1050) covalent geometry : bond 0.00580 ( 7835) covalent geometry : angle 0.63718 (10653) Misc. bond : bond 0.00032 ( 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 192 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 143 LEU cc_start: 0.8389 (mt) cc_final: 0.8178 (mp) REVERT: B 325 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6946 (mp0) REVERT: B 337 MET cc_start: 0.6809 (tpp) cc_final: 0.6251 (tpp) REVERT: B 388 LEU cc_start: 0.4154 (OUTLIER) cc_final: 0.3910 (tp) REVERT: B 487 TRP cc_start: 0.6840 (m100) cc_final: 0.6289 (m100) REVERT: A 391 TRP cc_start: 0.8019 (OUTLIER) cc_final: 0.6522 (t60) outliers start: 33 outliers final: 23 residues processed: 175 average time/residue: 0.1638 time to fit residues: 39.9334 Evaluate side-chains 180 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 85 ASP 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 263 MET 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: 0.6980 chunk 33 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 79 optimal weight: 0.6980 chunk 36 optimal weight: 0.0370 chunk 16 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.162393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.138535 restraints weight = 26616.068| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 4.00 r_work: 0.3613 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- 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 = 0.30 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 = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7837 Z= 0.188 Angle : 0.608 8.196 10653 Z= 0.308 Chirality : 0.044 0.197 1193 Planarity : 0.005 0.055 1386 Dihedral : 6.883 70.195 1088 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.33 % Allowed : 25.15 % 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 (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: -0.07 (0.28), residues: 961 helix: 1.10 (0.25), residues: 379 sheet: -0.29 (0.44), residues: 149 loop : -0.95 (0.32), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 0.002 0.000 ARG A 439 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 378) hydrogen bonds : angle 5.66892 ( 1050) covalent geometry : bond 0.00436 ( 7835) covalent geometry : angle 0.60772 (10653) Misc. bond : bond 0.00031 ( 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 195 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 337 MET cc_start: 0.7083 (tpp) cc_final: 0.6421 (tpp) REVERT: B 388 LEU cc_start: 0.4291 (tp) cc_final: 0.4027 (tp) REVERT: B 487 TRP cc_start: 0.7064 (m100) cc_final: 0.6261 (m100) REVERT: A 319 GLU cc_start: 0.7026 (tm-30) cc_final: 0.6783 (tm-30) outliers start: 36 outliers final: 24 residues processed: 179 average time/residue: 0.1768 time to fit residues: 44.0279 Evaluate side-chains 175 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 90 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 74 optimal weight: 0.0980 chunk 80 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 95 optimal weight: 0.1980 chunk 32 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4082 r_free = 0.4082 target = 0.162428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.138660 restraints weight = 22646.245| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 3.55 r_work: 0.3627 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1540 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= 0.182 Angle : 0.601 8.890 10653 Z= 0.305 Chirality : 0.043 0.179 1193 Planarity : 0.005 0.058 1386 Dihedral : 6.963 78.075 1088 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.33 % Allowed : 24.91 % Favored : 70.76 % 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: 1.14 (0.25), residues: 379 sheet: -0.30 (0.43), residues: 149 loop : -0.94 (0.32), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 487 HIS 0.004 0.001 HIS B 30 PHE 0.012 0.002 PHE A 493 TYR 0.016 0.001 TYR A 409 ARG 0.002 0.000 ARG A 439 Details of bonding type rmsd hydrogen bonds : bond 0.03778 ( 378) hydrogen bonds : angle 5.61370 ( 1050) covalent geometry : bond 0.00421 ( 7835) covalent geometry : angle 0.60079 (10653) 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 187 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLN cc_start: 0.7581 (mp10) cc_final: 0.7305 (mp10) REVERT: B 337 MET cc_start: 0.7101 (tpp) cc_final: 0.6386 (tpp) REVERT: B 487 TRP cc_start: 0.7046 (m100) cc_final: 0.6256 (m100) REVERT: A 319 GLU cc_start: 0.7157 (tm-30) cc_final: 0.6887 (tm-30) REVERT: A 505 ASN cc_start: 0.7904 (t0) cc_final: 0.7539 (t0) outliers start: 35 outliers final: 25 residues processed: 170 average time/residue: 0.1733 time to fit residues: 41.1541 Evaluate side-chains 176 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 71 optimal weight: 0.0980 chunk 84 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 chunk 33 optimal weight: 0.0050 overall best weight: 0.3994 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.167049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.143542 restraints weight = 23963.329| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 3.57 r_work: 0.3627 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- 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 = 0.21 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 = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.1652 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 : 0.588 9.412 10653 Z= 0.295 Chirality : 0.043 0.180 1193 Planarity : 0.005 0.057 1386 Dihedral : 6.972 88.274 1088 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.73 % Allowed : 25.27 % 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: 0.08 (0.28), residues: 961 helix: 1.26 (0.26), residues: 379 sheet: -0.25 (0.44), residues: 149 loop : -0.90 (0.32), residues: 433 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 0.009 0.001 TYR A 172 ARG 0.002 0.000 ARG A 439 Details of bonding type rmsd hydrogen bonds : bond 0.03468 ( 378) hydrogen bonds : angle 5.44734 ( 1050) covalent geometry : bond 0.00359 ( 7835) covalent geometry : angle 0.58796 (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 185 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 337 MET cc_start: 0.7093 (tpp) cc_final: 0.6429 (tpp) REVERT: B 487 TRP cc_start: 0.7048 (m100) cc_final: 0.6273 (m100) REVERT: A 319 GLU cc_start: 0.7176 (tm-30) cc_final: 0.6891 (tm-30) REVERT: A 337 MET cc_start: 0.7337 (ttt) cc_final: 0.7072 (tpp) REVERT: A 505 ASN cc_start: 0.7909 (t0) cc_final: 0.7531 (t0) outliers start: 30 outliers final: 25 residues processed: 173 average time/residue: 0.1813 time to fit residues: 43.6659 Evaluate side-chains 179 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 47 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.0010 chunk 34 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.162522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.138811 restraints weight = 22771.638| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 3.58 r_work: 0.3620 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3627 r_free = 0.3627 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3627 r_free = 0.3627 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1692 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= 0.179 Angle : 0.610 9.884 10653 Z= 0.305 Chirality : 0.043 0.177 1193 Planarity : 0.005 0.058 1386 Dihedral : 6.832 65.309 1088 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.09 % Allowed : 25.27 % Favored : 70.64 % 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: 0.06 (0.28), residues: 961 helix: 1.26 (0.26), residues: 380 sheet: -0.25 (0.44), residues: 149 loop : -0.93 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 487 HIS 0.005 0.001 HIS A 30 PHE 0.012 0.002 PHE A 493 TYR 0.012 0.001 TYR A 409 ARG 0.003 0.000 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 378) hydrogen bonds : angle 5.46075 ( 1050) covalent geometry : bond 0.00415 ( 7835) covalent geometry : angle 0.60977 (10653) Misc. bond : bond 0.00029 ( 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 187 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLN cc_start: 0.7625 (mp10) cc_final: 0.7341 (mp10) REVERT: B 337 MET cc_start: 0.7114 (tpp) cc_final: 0.6474 (tpp) REVERT: B 487 TRP cc_start: 0.7067 (m100) cc_final: 0.6285 (m100) REVERT: A 40 GLU cc_start: 0.6405 (mt-10) cc_final: 0.6035 (tt0) REVERT: A 319 GLU cc_start: 0.7182 (tm-30) cc_final: 0.6918 (tm-30) REVERT: A 505 ASN cc_start: 0.7906 (t0) cc_final: 0.7549 (t0) outliers start: 33 outliers final: 27 residues processed: 172 average time/residue: 0.1717 time to fit residues: 41.1958 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 : 0.804 ------------------------------------------------------------------------------- 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 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 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 510 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 62 optimal weight: 0.5980 chunk 44 optimal weight: 0.0970 chunk 38 optimal weight: 0.1980 chunk 2 optimal weight: 0.5980 chunk 33 optimal weight: 0.1980 chunk 87 optimal weight: 0.3980 chunk 74 optimal weight: 0.2980 chunk 57 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 overall best weight: 0.2378 ------------------------------------------------------------------------------- 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 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 = 0.4107 r_free = 0.4107 target = 0.164696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.141591 restraints weight = 20003.981| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 3.33 r_work: 0.3676 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3677 r_free = 0.3677 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3677 r_free = 0.3677 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7837 Z= 0.121 Angle : 0.577 9.974 10653 Z= 0.286 Chirality : 0.042 0.175 1193 Planarity : 0.005 0.057 1386 Dihedral : 6.871 79.360 1088 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.37 % Allowed : 25.63 % 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: 0.27 (0.28), residues: 961 helix: 1.43 (0.26), residues: 385 sheet: -0.23 (0.42), residues: 157 loop : -0.80 (0.33), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.004 0.001 HIS A 30 PHE 0.011 0.001 PHE A 493 TYR 0.019 0.001 TYR A 409 ARG 0.002 0.000 ARG A 439 Details of bonding type rmsd hydrogen bonds : bond 0.03134 ( 378) hydrogen bonds : angle 5.20737 ( 1050) covalent geometry : bond 0.00279 ( 7835) covalent geometry : angle 0.57741 (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 183 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLN cc_start: 0.7530 (mp10) cc_final: 0.7256 (mp10) REVERT: B 142 GLN cc_start: 0.8063 (mm110) cc_final: 0.7794 (mt0) REVERT: B 337 MET cc_start: 0.7019 (tpp) cc_final: 0.6436 (tpp) REVERT: B 487 TRP cc_start: 0.7006 (m100) cc_final: 0.6071 (m100) REVERT: A 319 GLU cc_start: 0.7152 (tm-30) cc_final: 0.6881 (tm-30) REVERT: A 505 ASN cc_start: 0.7853 (t0) cc_final: 0.7477 (t0) outliers start: 27 outliers final: 23 residues processed: 171 average time/residue: 0.1844 time to fit residues: 43.0676 Evaluate side-chains 177 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU 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 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 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: 0.5980 chunk 1 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 34 optimal weight: 0.4980 chunk 89 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 44 optimal weight: 0.0870 chunk 57 optimal weight: 0.0870 chunk 78 optimal weight: 0.8980 overall best weight: 0.3736 ------------------------------------------------------------------------------- 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 = 0.4117 r_free = 0.4117 target = 0.167610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.141948 restraints weight = 31384.765| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 4.48 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3772 r_free = 0.3772 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3772 r_free = 0.3772 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7837 Z= 0.151 Angle : 0.612 10.228 10653 Z= 0.299 Chirality : 0.043 0.174 1193 Planarity : 0.005 0.057 1386 Dihedral : 7.023 87.292 1088 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.37 % Allowed : 25.63 % 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: 1.42 (0.26), residues: 385 sheet: -0.10 (0.43), residues: 149 loop : -0.83 (0.33), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 487 HIS 0.004 0.001 HIS A 30 PHE 0.012 0.002 PHE A 493 TYR 0.013 0.001 TYR A 409 ARG 0.002 0.000 ARG A 439 Details of bonding type rmsd hydrogen bonds : bond 0.03271 ( 378) hydrogen bonds : angle 5.23687 ( 1050) covalent geometry : bond 0.00354 ( 7835) covalent geometry : angle 0.61188 (10653) Misc. bond : bond 0.00028 ( 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 177 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLN cc_start: 0.7414 (mp10) cc_final: 0.7142 (mp10) REVERT: B 142 GLN cc_start: 0.7976 (mm110) cc_final: 0.7696 (mt0) REVERT: B 337 MET cc_start: 0.6556 (tpp) cc_final: 0.6053 (tpp) REVERT: B 487 TRP cc_start: 0.6594 (m100) cc_final: 0.5682 (m100) REVERT: A 319 GLU cc_start: 0.6742 (tm-30) cc_final: 0.6527 (tm-30) REVERT: A 505 ASN cc_start: 0.7282 (t0) cc_final: 0.6962 (t0) outliers start: 27 outliers final: 23 residues processed: 165 average time/residue: 0.1737 time to fit residues: 39.6253 Evaluate side-chains 170 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 12 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 52 optimal weight: 0.6980 chunk 16 optimal weight: 0.0970 chunk 34 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 chunk 67 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 21 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 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 = 0.4123 r_free = 0.4123 target = 0.167991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.146943 restraints weight = 13745.970| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.66 r_work: 0.3718 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.1831 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= 0.139 Angle : 0.612 10.718 10653 Z= 0.299 Chirality : 0.042 0.173 1193 Planarity : 0.005 0.057 1386 Dihedral : 7.058 88.215 1088 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.37 % Allowed : 25.63 % 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: 0.30 (0.28), residues: 961 helix: 1.43 (0.25), residues: 383 sheet: -0.17 (0.42), residues: 157 loop : -0.77 (0.33), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 487 HIS 0.004 0.001 HIS A 30 PHE 0.012 0.001 PHE B 199 TYR 0.012 0.001 TYR A 409 ARG 0.002 0.000 ARG A 439 Details of bonding type rmsd hydrogen bonds : bond 0.03259 ( 378) hydrogen bonds : angle 5.21630 ( 1050) covalent geometry : bond 0.00324 ( 7835) covalent geometry : angle 0.61182 (10653) Misc. bond : bond 0.00028 ( 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 174 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLN cc_start: 0.7532 (mp10) cc_final: 0.7251 (mp10) REVERT: B 142 GLN cc_start: 0.8042 (mm110) cc_final: 0.7780 (mt0) REVERT: B 337 MET cc_start: 0.6980 (tpp) cc_final: 0.6393 (tpp) REVERT: B 475 ILE cc_start: 0.7936 (mt) cc_final: 0.7639 (tt) REVERT: B 487 TRP cc_start: 0.6930 (m100) cc_final: 0.6095 (m100) REVERT: A 319 GLU cc_start: 0.7032 (tm-30) cc_final: 0.6780 (tm-30) REVERT: A 505 ASN cc_start: 0.7758 (t0) cc_final: 0.7392 (t0) outliers start: 27 outliers final: 25 residues processed: 161 average time/residue: 0.1949 time to fit residues: 43.9846 Evaluate side-chains 170 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LEU 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 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 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 24 optimal weight: 0.0970 chunk 88 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 13 optimal weight: 0.0870 chunk 73 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 19 optimal weight: 0.2980 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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 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 = 0.4094 r_free = 0.4094 target = 0.163557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.139641 restraints weight = 22691.562| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 3.59 r_work: 0.3628 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3628 ------------------------------------------------------------------------------- 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 = 0.18 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 = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.1848 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= 0.164 Angle : 0.612 10.595 10653 Z= 0.302 Chirality : 0.043 0.172 1193 Planarity : 0.005 0.057 1386 Dihedral : 6.960 88.658 1088 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.49 % Allowed : 25.63 % 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: 0.22 (0.28), residues: 961 helix: 1.34 (0.26), residues: 385 sheet: -0.02 (0.44), residues: 143 loop : -0.88 (0.32), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 487 HIS 0.004 0.001 HIS A 30 PHE 0.012 0.002 PHE A 493 TYR 0.011 0.001 TYR A 409 ARG 0.002 0.000 ARG A 141 Details of bonding type rmsd hydrogen bonds : bond 0.03359 ( 378) hydrogen bonds : angle 5.25762 ( 1050) covalent geometry : bond 0.00382 ( 7835) covalent geometry : angle 0.61227 (10653) Misc. bond : bond 0.00028 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4728.07 seconds wall clock time: 82 minutes 51.26 seconds (4971.26 seconds total)