Starting phenix.real_space_refine on Thu Nov 14 22:59:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u64_41943/11_2024/8u64_41943.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u64_41943/11_2024/8u64_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u64_41943/11_2024/8u64_41943.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u64_41943/11_2024/8u64_41943.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u64_41943/11_2024/8u64_41943.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u64_41943/11_2024/8u64_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 2.80, per 1000 atoms: 0.36 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: 2.18 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: 0.80 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: 2.30 Time building geometry restraints manager: 2.42 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: 22.810 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 17.360 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.420 ------------------------------------------------------------------------------- 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 0.051 7835 Z= 0.231 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 *********************** 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 : 0.812 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: 0.1961 time to fit residues: 40.0607 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 : 0.827 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 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 7835 Z= 0.175 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 *********************** 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 : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLN cc_start: 0.7639 (mp10) cc_final: 0.7401 (mp10) REVERT: B 325 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: B 337 MET cc_start: 0.6883 (tpp) cc_final: 0.6530 (tpp) REVERT: B 487 TRP cc_start: 0.6829 (m100) cc_final: 0.6135 (m100) REVERT: A 391 TRP cc_start: 0.7957 (OUTLIER) cc_final: 0.6880 (t60) outliers start: 23 outliers final: 11 residues processed: 165 average time/residue: 0.1792 time to fit residues: 40.7640 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 : 0.785 ------------------------------------------------------------------------------- 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 48 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 87 optimal weight: 0.0670 chunk 94 optimal weight: 0.9980 chunk 77 optimal weight: 0.4980 chunk 86 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 70 optimal weight: 0.0050 overall best weight: 0.3132 ------------------------------------------------------------------------------- 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 215 ASN A 306 GLN A 323 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7835 Z= 0.208 Angle : 0.551 8.070 10653 Z= 0.281 Chirality : 0.042 0.136 1193 Planarity : 0.005 0.047 1386 Dihedral : 6.714 67.618 1088 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.13 % Allowed : 24.67 % 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: 0.16 (0.28), residues: 961 helix: 1.23 (0.25), residues: 387 sheet: -0.18 (0.42), residues: 157 loop : -0.81 (0.33), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 448 HIS 0.004 0.001 HIS A 30 PHE 0.012 0.001 PHE A 493 TYR 0.009 0.001 TYR A 409 ARG 0.002 0.000 ARG B 168 *********************** 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 178 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLN cc_start: 0.7614 (mp10) cc_final: 0.7348 (mp10) REVERT: B 337 MET cc_start: 0.6860 (tpp) cc_final: 0.6347 (tpp) REVERT: B 487 TRP cc_start: 0.6865 (m100) cc_final: 0.6240 (m100) outliers start: 26 outliers final: 16 residues processed: 167 average time/residue: 0.1843 time to fit residues: 42.5652 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 : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 VAL 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 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 86 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 87 optimal weight: 0.0570 chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 0.0970 overall best weight: 0.4296 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7835 Z= 0.251 Angle : 0.593 10.858 10653 Z= 0.296 Chirality : 0.043 0.139 1193 Planarity : 0.005 0.050 1386 Dihedral : 6.655 66.133 1088 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.97 % Allowed : 24.67 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.28), residues: 961 helix: 1.33 (0.26), residues: 379 sheet: -0.13 (0.43), residues: 154 loop : -0.81 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 487 HIS 0.005 0.001 HIS A 30 PHE 0.013 0.002 PHE A 493 TYR 0.009 0.001 TYR A 172 ARG 0.002 0.000 ARG A 168 *********************** 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 185 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 337 MET cc_start: 0.6941 (tpp) cc_final: 0.6324 (tpp) REVERT: B 487 TRP cc_start: 0.6879 (m100) cc_final: 0.6187 (m100) outliers start: 33 outliers final: 21 residues processed: 171 average time/residue: 0.1717 time to fit residues: 41.0400 Evaluate side-chains 170 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 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 52 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 38 optimal weight: 0.2980 chunk 79 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 83 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 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 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7835 Z= 0.276 Angle : 0.598 9.187 10653 Z= 0.300 Chirality : 0.043 0.137 1193 Planarity : 0.005 0.053 1386 Dihedral : 6.848 80.312 1088 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.13 % Allowed : 25.75 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.28), residues: 961 helix: 1.29 (0.26), residues: 379 sheet: -0.26 (0.41), residues: 161 loop : -0.82 (0.33), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 487 HIS 0.005 0.001 HIS A 30 PHE 0.012 0.002 PHE A 493 TYR 0.015 0.001 TYR A 409 ARG 0.002 0.000 ARG A 214 *********************** 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 179 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLN cc_start: 0.7589 (mp10) cc_final: 0.7355 (mp10) REVERT: B 191 MET cc_start: 0.5615 (OUTLIER) cc_final: 0.5410 (ttm) REVERT: B 337 MET cc_start: 0.6994 (tpp) cc_final: 0.6312 (tpp) REVERT: B 487 TRP cc_start: 0.6905 (m100) cc_final: 0.6131 (m100) REVERT: A 505 ASN cc_start: 0.7838 (t0) cc_final: 0.7468 (t0) outliers start: 26 outliers final: 21 residues processed: 165 average time/residue: 0.1870 time to fit residues: 42.9949 Evaluate side-chains 172 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 191 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 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 360 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 7835 Z= 0.357 Angle : 0.640 9.469 10653 Z= 0.321 Chirality : 0.044 0.191 1193 Planarity : 0.005 0.057 1386 Dihedral : 7.124 82.951 1088 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.21 % Allowed : 24.79 % 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: -0.09 (0.28), residues: 961 helix: 1.15 (0.25), residues: 380 sheet: -0.45 (0.42), residues: 153 loop : -0.98 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 487 HIS 0.006 0.001 HIS B 30 PHE 0.012 0.002 PHE A 438 TYR 0.011 0.002 TYR A 172 ARG 0.003 0.000 ARG B 168 *********************** 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 189 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 337 MET cc_start: 0.7019 (tpp) cc_final: 0.6357 (tpp) REVERT: B 487 TRP cc_start: 0.6933 (m100) cc_final: 0.6426 (m100) REVERT: A 505 ASN cc_start: 0.7864 (t0) cc_final: 0.7517 (t0) outliers start: 34 outliers final: 26 residues processed: 173 average time/residue: 0.1815 time to fit residues: 44.0643 Evaluate side-chains 178 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 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 510 GLN Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 360 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 chunk 78 optimal weight: 0.5980 chunk 51 optimal weight: 0.4980 chunk 92 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 36 optimal weight: 0.0670 chunk 55 optimal weight: 0.0770 overall best weight: 0.3276 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7835 Z= 0.217 Angle : 0.590 9.777 10653 Z= 0.291 Chirality : 0.042 0.181 1193 Planarity : 0.005 0.057 1386 Dihedral : 6.856 69.319 1088 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.33 % Allowed : 24.79 % 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: 0.14 (0.28), residues: 961 helix: 1.32 (0.25), residues: 386 sheet: -0.27 (0.43), residues: 156 loop : -0.88 (0.33), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 448 HIS 0.004 0.001 HIS A 30 PHE 0.011 0.002 PHE B 199 TYR 0.014 0.001 TYR A 409 ARG 0.004 0.000 ARG B 288 *********************** 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 192 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLN cc_start: 0.7545 (mp10) cc_final: 0.7308 (mp10) REVERT: B 337 MET cc_start: 0.6994 (tpp) cc_final: 0.6393 (tpp) REVERT: B 487 TRP cc_start: 0.6917 (m100) cc_final: 0.6136 (m100) REVERT: A 505 ASN cc_start: 0.7813 (t0) cc_final: 0.7453 (t0) outliers start: 35 outliers final: 26 residues processed: 175 average time/residue: 0.1994 time to fit residues: 48.5435 Evaluate side-chains 181 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 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 389 HIS 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 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 27 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 63 optimal weight: 0.4980 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 ASN 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 7835 Z= 0.343 Angle : 0.644 10.212 10653 Z= 0.322 Chirality : 0.044 0.183 1193 Planarity : 0.005 0.058 1386 Dihedral : 7.215 87.109 1088 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.37 % Allowed : 25.39 % 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 (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: 0.03 (0.28), residues: 961 helix: 1.21 (0.25), residues: 380 sheet: -0.23 (0.43), residues: 155 loop : -0.94 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 487 HIS 0.005 0.001 HIS B 30 PHE 0.012 0.002 PHE A 438 TYR 0.019 0.002 TYR A 409 ARG 0.002 0.000 ARG A 439 *********************** 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 187 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLN cc_start: 0.7574 (mp10) cc_final: 0.7264 (mp10) REVERT: B 337 MET cc_start: 0.7022 (tpp) cc_final: 0.6408 (tpp) REVERT: B 487 TRP cc_start: 0.6951 (m100) cc_final: 0.6248 (m100) REVERT: A 505 ASN cc_start: 0.7828 (t0) cc_final: 0.7490 (t0) outliers start: 27 outliers final: 25 residues processed: 172 average time/residue: 0.1813 time to fit residues: 43.2775 Evaluate side-chains 183 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 chunk 37 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 7835 Z= 0.329 Angle : 0.657 10.499 10653 Z= 0.325 Chirality : 0.044 0.181 1193 Planarity : 0.005 0.059 1386 Dihedral : 7.000 65.706 1088 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.13 % Allowed : 25.39 % Favored : 71.48 % 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: 1.16 (0.25), residues: 380 sheet: -0.32 (0.42), residues: 154 loop : -0.97 (0.32), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 487 HIS 0.005 0.001 HIS B 30 PHE 0.012 0.002 PHE A 198 TYR 0.011 0.002 TYR A 409 ARG 0.004 0.000 ARG B 214 *********************** 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 179 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 337 MET cc_start: 0.7031 (tpp) cc_final: 0.6368 (tpp) REVERT: B 487 TRP cc_start: 0.6959 (m100) cc_final: 0.6230 (m100) REVERT: A 505 ASN cc_start: 0.7834 (t0) cc_final: 0.7493 (t0) outliers start: 25 outliers final: 23 residues processed: 165 average time/residue: 0.1914 time to fit residues: 43.1324 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 : 0.871 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.2980 chunk 43 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 A 306 GLN ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 7835 Z= 0.323 Angle : 0.660 10.218 10653 Z= 0.327 Chirality : 0.044 0.180 1193 Planarity : 0.006 0.059 1386 Dihedral : 7.066 69.930 1088 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.37 % Allowed : 25.27 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.28), residues: 961 helix: 1.14 (0.25), residues: 380 sheet: -0.29 (0.42), residues: 155 loop : -0.98 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 487 HIS 0.005 0.001 HIS B 30 PHE 0.014 0.002 PHE A 346 TYR 0.011 0.002 TYR A 172 ARG 0.008 0.000 ARG B 288 ********************** 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 183 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLN cc_start: 0.7540 (mp10) cc_final: 0.7294 (mp10) REVERT: B 191 MET cc_start: 0.5887 (mtm) cc_final: 0.5488 (mtt) REVERT: B 337 MET cc_start: 0.7004 (tpp) cc_final: 0.6419 (tpp) REVERT: B 487 TRP cc_start: 0.6960 (m100) cc_final: 0.6325 (m100) REVERT: A 505 ASN cc_start: 0.7834 (t0) cc_final: 0.7491 (t0) outliers start: 27 outliers final: 23 residues processed: 168 average time/residue: 0.1922 time to fit residues: 44.9638 Evaluate side-chains 174 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.3980 chunk 70 optimal weight: 0.1980 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 chunk 78 optimal weight: 0.5980 chunk 9 optimal weight: 0.2980 chunk 14 optimal weight: 0.7980 chunk 66 optimal weight: 0.0980 chunk 4 optimal weight: 0.0980 overall best weight: 0.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN B 351 GLN B 352 GLN A 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 = 0.4078 r_free = 0.4078 target = 0.162182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.140352 restraints weight = 16272.600| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.90 r_work: 0.3666 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- 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 = 0.37 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 = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.190 7835 Z= 0.334 Angle : 1.030 59.175 10653 Z= 0.597 Chirality : 0.047 0.684 1193 Planarity : 0.006 0.066 1386 Dihedral : 7.154 70.140 1088 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.01 % Allowed : 25.87 % Favored : 71.12 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.15 (0.25), residues: 380 sheet: -0.29 (0.42), residues: 155 loop : -0.98 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 487 HIS 0.005 0.001 HIS B 30 PHE 0.012 0.002 PHE A 346 TYR 0.009 0.001 TYR A 172 ARG 0.005 0.000 ARG B 288 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2519.70 seconds wall clock time: 46 minutes 38.77 seconds (2798.77 seconds total)