Starting phenix.real_space_refine on Thu Jun 27 08:11:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsg_32757/06_2024/7wsg_32757.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsg_32757/06_2024/7wsg_32757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsg_32757/06_2024/7wsg_32757.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsg_32757/06_2024/7wsg_32757.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsg_32757/06_2024/7wsg_32757.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsg_32757/06_2024/7wsg_32757.pdb" } resolution = 3.03 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= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5903 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4102 2.51 5 N 1067 2.21 5 O 1206 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 38": "OE1" <-> "OE2" Residue "A TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 201": "OD1" <-> "OD2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 499": "OD1" <-> "OD2" Residue "A ASP 580": "OD1" <-> "OD2" Residue "B PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 6413 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4885 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 567} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1527 Classifications: {'peptide': 190} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 177} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.39, per 1000 atoms: 0.68 Number of scatterers: 6413 At special positions: 0 Unit cell: (80.949, 83.625, 120.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1206 8.00 N 1067 7.00 C 4102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1486 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 4 sheets defined 53.2% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 20 through 27 Processing helix chain 'A' and resid 27 through 53 removed outlier: 4.091A pdb=" N ASN A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 82 removed outlier: 3.611A pdb=" N TRP A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.647A pdb=" N LYS A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A 99 " --> pdb=" O ARG A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.777A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 removed outlier: 3.653A pdb=" N ARG A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 154 removed outlier: 4.081A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 171 removed outlier: 3.585A pdb=" N TRP A 163 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 194 Proline residue: A 178 - end of helix removed outlier: 3.620A pdb=" N ASN A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 218 through 252 removed outlier: 4.097A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.935A pdb=" N ASP A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 304 through 318 removed outlier: 3.806A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.838A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 386 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.866A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.628A pdb=" N ASN A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 450 removed outlier: 3.532A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 464 removed outlier: 4.478A pdb=" N GLU A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 474 removed outlier: 3.530A pdb=" N TRP A 473 " --> pdb=" O LYS A 470 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N MET A 474 " --> pdb=" O GLU A 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 470 through 474' Processing helix chain 'A' and resid 475 through 485 removed outlier: 3.523A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 531 removed outlier: 4.600A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 560 removed outlier: 3.694A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N MET A 557 " --> pdb=" O THR A 553 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A 560 " --> pdb=" O GLN A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.711A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 371 through 375 removed outlier: 3.573A pdb=" N LEU B 374 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 371 through 375' Processing helix chain 'B' and resid 425 through 430 Processing helix chain 'B' and resid 488 through 491 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.401A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA3, first strand: chain 'B' and resid 341 through 343 removed outlier: 3.539A pdb=" N ALA B 384 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG B 495 " --> pdb=" O TRP B 423 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP B 423 " --> pdb=" O ARG B 495 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 439 through 441 263 hydrogen bonds defined for protein. 759 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: 1.56 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2060 1.34 - 1.46: 1669 1.46 - 1.58: 2813 1.58 - 1.70: 0 1.70 - 1.81: 59 Bond restraints: 6601 Sorted by residual: bond pdb=" CA VAL B 507 " pdb=" CB VAL B 507 " ideal model delta sigma weight residual 1.540 1.527 0.013 1.36e-02 5.41e+03 9.20e-01 bond pdb=" CB THR A 453 " pdb=" CG2 THR A 453 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.20e-01 bond pdb=" CG1 ILE A 379 " pdb=" CD1 ILE A 379 " ideal model delta sigma weight residual 1.513 1.488 0.025 3.90e-02 6.57e+02 4.06e-01 bond pdb=" CB PRO B 470 " pdb=" CG PRO B 470 " ideal model delta sigma weight residual 1.506 1.482 0.024 3.90e-02 6.57e+02 3.64e-01 bond pdb=" N THR B 468 " pdb=" CA THR B 468 " ideal model delta sigma weight residual 1.460 1.453 0.007 1.29e-02 6.01e+03 3.15e-01 ... (remaining 6596 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.89: 238 106.89 - 113.68: 3470 113.68 - 120.46: 2666 120.46 - 127.25: 2491 127.25 - 134.04: 107 Bond angle restraints: 8972 Sorted by residual: angle pdb=" N ALA A 304 " pdb=" CA ALA A 304 " pdb=" C ALA A 304 " ideal model delta sigma weight residual 114.62 110.96 3.66 1.14e+00 7.69e-01 1.03e+01 angle pdb=" CA ALA A 304 " pdb=" C ALA A 304 " pdb=" N ARG A 305 " ideal model delta sigma weight residual 119.71 116.33 3.38 1.17e+00 7.31e-01 8.34e+00 angle pdb=" CA LEU A 266 " pdb=" CB LEU A 266 " pdb=" CG LEU A 266 " ideal model delta sigma weight residual 116.30 124.49 -8.19 3.50e+00 8.16e-02 5.48e+00 angle pdb=" CA LEU B 421 " pdb=" CB LEU B 421 " pdb=" CG LEU B 421 " ideal model delta sigma weight residual 116.30 124.30 -8.00 3.50e+00 8.16e-02 5.23e+00 angle pdb=" CA TYR A 385 " pdb=" CB TYR A 385 " pdb=" CG TYR A 385 " ideal model delta sigma weight residual 113.90 117.91 -4.01 1.80e+00 3.09e-01 4.95e+00 ... (remaining 8967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.40: 3563 16.40 - 32.80: 252 32.80 - 49.20: 54 49.20 - 65.60: 24 65.60 - 82.00: 5 Dihedral angle restraints: 3898 sinusoidal: 1582 harmonic: 2316 Sorted by residual: dihedral pdb=" CA ALA A 396 " pdb=" C ALA A 396 " pdb=" N ASN A 397 " pdb=" CA ASN A 397 " ideal model delta harmonic sigma weight residual 180.00 162.19 17.81 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA LYS A 475 " pdb=" C LYS A 475 " pdb=" N LYS A 476 " pdb=" CA LYS A 476 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ASP A 499 " pdb=" CB ASP A 499 " pdb=" CG ASP A 499 " pdb=" OD1 ASP A 499 " ideal model delta sinusoidal sigma weight residual -30.00 -85.77 55.77 1 2.00e+01 2.50e-03 1.05e+01 ... (remaining 3895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 485 0.026 - 0.052: 283 0.052 - 0.078: 100 0.078 - 0.103: 47 0.103 - 0.129: 11 Chirality restraints: 926 Sorted by residual: chirality pdb=" CG LEU A 266 " pdb=" CB LEU A 266 " pdb=" CD1 LEU A 266 " pdb=" CD2 LEU A 266 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA VAL B 420 " pdb=" N VAL B 420 " pdb=" C VAL B 420 " pdb=" CB VAL B 420 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.18e-01 chirality pdb=" CA PRO B 477 " pdb=" N PRO B 477 " pdb=" C PRO B 477 " pdb=" CB PRO B 477 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.04e-01 ... (remaining 923 not shown) Planarity restraints: 1163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 145 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO A 146 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 489 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO A 490 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 490 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 490 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 291 " -0.006 2.00e-02 2.50e+03 1.25e-02 1.57e+00 pdb=" C ILE A 291 " 0.022 2.00e-02 2.50e+03 pdb=" O ILE A 291 " -0.008 2.00e-02 2.50e+03 pdb=" N ASP A 292 " -0.007 2.00e-02 2.50e+03 ... (remaining 1160 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 81 2.63 - 3.19: 5785 3.19 - 3.76: 10416 3.76 - 4.33: 14655 4.33 - 4.90: 23875 Nonbonded interactions: 54812 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 901 " model vdw 2.058 2.230 nonbonded pdb=" O THR A 125 " pdb=" OG1 THR A 129 " model vdw 2.207 2.440 nonbonded pdb=" O THR A 449 " pdb=" OG1 THR A 453 " model vdw 2.226 2.440 nonbonded pdb=" NH1 ARG A 245 " pdb=" O PRO A 258 " model vdw 2.235 2.520 nonbonded pdb=" OG1 THR A 276 " pdb=" OG1 THR A 445 " model vdw 2.245 2.440 ... (remaining 54807 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 9.830 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.860 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 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 : 0.003 0.025 6601 Z= 0.167 Angle : 0.524 8.195 8972 Z= 0.275 Chirality : 0.039 0.129 926 Planarity : 0.003 0.039 1163 Dihedral : 12.816 81.998 2394 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.60 % Allowed : 11.08 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -1.05 (0.29), residues: 783 helix: -0.44 (0.27), residues: 344 sheet: -1.89 (1.09), residues: 23 loop : -0.76 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 328 HIS 0.006 0.001 HIS A 241 PHE 0.009 0.001 PHE A 369 TYR 0.020 0.001 TYR A 385 ARG 0.004 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 139 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 LEU cc_start: 0.6706 (OUTLIER) cc_final: 0.6266 (mp) REVERT: A 480 MET cc_start: 0.6049 (OUTLIER) cc_final: 0.5717 (mtp) REVERT: A 552 GLN cc_start: 0.7338 (mt0) cc_final: 0.7028 (pt0) REVERT: A 597 GLU cc_start: 0.8382 (tt0) cc_final: 0.7917 (tm-30) REVERT: B 365 LYS cc_start: 0.7484 (ttmt) cc_final: 0.7103 (mtpp) REVERT: B 396 GLN cc_start: 0.6986 (OUTLIER) cc_final: 0.6632 (mt0) REVERT: B 498 VAL cc_start: 0.7580 (t) cc_final: 0.7343 (m) outliers start: 32 outliers final: 14 residues processed: 159 average time/residue: 0.2014 time to fit residues: 41.4132 Evaluate side-chains 120 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 505 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6601 Z= 0.222 Angle : 0.603 8.105 8972 Z= 0.312 Chirality : 0.043 0.201 926 Planarity : 0.004 0.035 1163 Dihedral : 7.390 61.648 891 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.88 % Allowed : 15.11 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -1.03 (0.28), residues: 783 helix: -0.28 (0.26), residues: 354 sheet: -1.74 (1.19), residues: 23 loop : -0.91 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 594 HIS 0.007 0.001 HIS A 241 PHE 0.024 0.002 PHE A 369 TYR 0.023 0.002 TYR A 385 ARG 0.003 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 552 GLN cc_start: 0.7146 (mt0) cc_final: 0.6882 (pt0) REVERT: A 597 GLU cc_start: 0.8187 (tt0) cc_final: 0.7737 (tm-30) REVERT: B 396 GLN cc_start: 0.6982 (OUTLIER) cc_final: 0.6670 (mt0) outliers start: 27 outliers final: 20 residues processed: 131 average time/residue: 0.1740 time to fit residues: 30.6900 Evaluate side-chains 115 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 505 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 70 optimal weight: 0.0670 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6601 Z= 0.174 Angle : 0.542 7.773 8972 Z= 0.279 Chirality : 0.040 0.133 926 Planarity : 0.004 0.038 1163 Dihedral : 6.764 57.347 884 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.32 % Allowed : 16.26 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.75 (0.29), residues: 783 helix: 0.02 (0.27), residues: 351 sheet: -1.51 (1.27), residues: 23 loop : -0.84 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.022 0.001 PHE B 364 TYR 0.020 0.001 TYR A 385 ARG 0.002 0.000 ARG B 495 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 107 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: A 597 GLU cc_start: 0.8160 (tt0) cc_final: 0.7720 (tm-30) REVERT: B 396 GLN cc_start: 0.6963 (OUTLIER) cc_final: 0.6716 (mt0) REVERT: B 452 GLU cc_start: 0.6465 (tt0) cc_final: 0.6229 (tt0) outliers start: 30 outliers final: 21 residues processed: 126 average time/residue: 0.1667 time to fit residues: 28.6620 Evaluate side-chains 117 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 95 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 473 TRP Chi-restraints excluded: chain A residue 495 GLU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 505 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 0.0670 chunk 75 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 0.0670 chunk 20 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 HIS ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6601 Z= 0.157 Angle : 0.535 8.342 8972 Z= 0.271 Chirality : 0.040 0.216 926 Planarity : 0.004 0.042 1163 Dihedral : 6.330 53.361 881 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.88 % Allowed : 18.13 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.61 (0.29), residues: 783 helix: 0.23 (0.27), residues: 351 sheet: -1.25 (1.30), residues: 23 loop : -0.86 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.016 0.001 PHE A 523 TYR 0.019 0.001 TYR A 385 ARG 0.004 0.000 ARG B 495 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 102 time to evaluate : 0.793 Fit side-chains revert: symmetry clash REVERT: A 597 GLU cc_start: 0.8147 (tt0) cc_final: 0.7709 (tm-30) REVERT: B 367 TYR cc_start: 0.6765 (m-80) cc_final: 0.6326 (m-80) outliers start: 27 outliers final: 23 residues processed: 121 average time/residue: 0.1545 time to fit residues: 25.8318 Evaluate side-chains 118 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 473 TRP Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain B residue 475 TYR Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 0.0370 chunk 64 optimal weight: 0.0030 chunk 52 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 67 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.4068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6601 Z= 0.148 Angle : 0.512 7.225 8972 Z= 0.260 Chirality : 0.040 0.172 926 Planarity : 0.004 0.050 1163 Dihedral : 5.731 48.297 878 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.74 % Allowed : 18.99 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.52 (0.29), residues: 783 helix: 0.32 (0.27), residues: 359 sheet: -1.10 (1.28), residues: 23 loop : -0.87 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.015 0.001 PHE A 523 TYR 0.018 0.001 TYR A 385 ARG 0.008 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 106 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 597 GLU cc_start: 0.8154 (tt0) cc_final: 0.7721 (tm-30) outliers start: 26 outliers final: 20 residues processed: 122 average time/residue: 0.1629 time to fit residues: 27.9766 Evaluate side-chains 116 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 473 TRP Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 475 TYR Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 0.0980 chunk 72 optimal weight: 0.0670 chunk 8 optimal weight: 0.6980 chunk 42 optimal weight: 0.0980 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6601 Z= 0.140 Angle : 0.507 6.704 8972 Z= 0.258 Chirality : 0.040 0.167 926 Planarity : 0.004 0.038 1163 Dihedral : 5.411 51.015 876 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.45 % Allowed : 18.99 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.42 (0.29), residues: 783 helix: 0.42 (0.28), residues: 359 sheet: -0.94 (1.27), residues: 23 loop : -0.83 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.015 0.001 PHE A 523 TYR 0.017 0.001 TYR A 385 ARG 0.005 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 101 time to evaluate : 0.677 Fit side-chains revert: symmetry clash REVERT: A 597 GLU cc_start: 0.8143 (tt0) cc_final: 0.7701 (tm-30) outliers start: 24 outliers final: 20 residues processed: 119 average time/residue: 0.1647 time to fit residues: 26.9965 Evaluate side-chains 112 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 473 TRP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 475 TYR Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 47 optimal weight: 0.0170 chunk 45 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6601 Z= 0.186 Angle : 0.532 6.360 8972 Z= 0.275 Chirality : 0.042 0.253 926 Planarity : 0.004 0.039 1163 Dihedral : 5.048 44.432 873 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.74 % Allowed : 18.71 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.45 (0.29), residues: 783 helix: 0.37 (0.27), residues: 359 sheet: -1.14 (1.24), residues: 23 loop : -0.81 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.017 0.001 PHE A 523 TYR 0.021 0.001 TYR A 385 ARG 0.005 0.000 ARG B 495 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 94 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 597 GLU cc_start: 0.8162 (tt0) cc_final: 0.7719 (tm-30) REVERT: B 341 GLU cc_start: 0.3834 (mt-10) cc_final: 0.3464 (mt-10) outliers start: 26 outliers final: 23 residues processed: 112 average time/residue: 0.1572 time to fit residues: 24.7265 Evaluate side-chains 108 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 85 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 473 TRP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 3.9990 chunk 47 optimal weight: 0.0570 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN A 378 HIS ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6601 Z= 0.222 Angle : 0.560 6.574 8972 Z= 0.288 Chirality : 0.043 0.263 926 Planarity : 0.004 0.038 1163 Dihedral : 5.244 46.833 873 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.17 % Allowed : 18.56 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.56 (0.29), residues: 783 helix: 0.22 (0.27), residues: 360 sheet: -1.42 (1.21), residues: 23 loop : -0.80 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 163 HIS 0.007 0.001 HIS A 241 PHE 0.015 0.001 PHE A 523 TYR 0.023 0.002 TYR A 385 ARG 0.005 0.000 ARG B 495 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 91 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 597 GLU cc_start: 0.8181 (tt0) cc_final: 0.7744 (tm-30) REVERT: B 341 GLU cc_start: 0.3855 (mt-10) cc_final: 0.3565 (mt-10) outliers start: 29 outliers final: 24 residues processed: 111 average time/residue: 0.1455 time to fit residues: 22.9981 Evaluate side-chains 110 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 473 TRP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 0.0980 chunk 66 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 46 optimal weight: 0.0570 chunk 74 optimal weight: 0.2980 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN A 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6601 Z= 0.152 Angle : 0.530 6.644 8972 Z= 0.271 Chirality : 0.041 0.248 926 Planarity : 0.004 0.038 1163 Dihedral : 4.992 41.853 873 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.60 % Allowed : 18.99 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.36 (0.29), residues: 783 helix: 0.44 (0.28), residues: 359 sheet: -1.33 (1.21), residues: 23 loop : -0.75 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.013 0.001 PHE A 523 TYR 0.018 0.001 TYR A 41 ARG 0.003 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 90 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: A 597 GLU cc_start: 0.8154 (tt0) cc_final: 0.7723 (tm-30) REVERT: B 341 GLU cc_start: 0.3766 (mt-10) cc_final: 0.3510 (mt-10) outliers start: 25 outliers final: 22 residues processed: 108 average time/residue: 0.1471 time to fit residues: 22.8626 Evaluate side-chains 109 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 473 TRP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain B residue 325 PHE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 475 TYR Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 0.0980 chunk 49 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 57 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6601 Z= 0.183 Angle : 0.537 6.358 8972 Z= 0.275 Chirality : 0.041 0.246 926 Planarity : 0.004 0.040 1163 Dihedral : 4.802 42.679 870 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.02 % Allowed : 19.57 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.29), residues: 783 helix: 0.39 (0.27), residues: 363 sheet: -1.43 (1.18), residues: 23 loop : -0.72 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.016 0.001 PHE A 523 TYR 0.020 0.002 TYR A 385 ARG 0.003 0.000 ARG A 177 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 89 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: A 221 GLN cc_start: 0.6522 (tt0) cc_final: 0.6124 (tt0) REVERT: A 484 LEU cc_start: 0.6672 (mt) cc_final: 0.6398 (mm) REVERT: A 597 GLU cc_start: 0.8192 (tt0) cc_final: 0.7749 (tm-30) REVERT: B 341 GLU cc_start: 0.3790 (mt-10) cc_final: 0.3543 (mt-10) REVERT: B 508 LEU cc_start: 0.3045 (OUTLIER) cc_final: 0.2677 (tm) outliers start: 21 outliers final: 18 residues processed: 103 average time/residue: 0.1474 time to fit residues: 21.6959 Evaluate side-chains 107 residues out of total 695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 88 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 473 TRP Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 63 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 3 optimal weight: 4.9990 chunk 44 optimal weight: 0.0980 chunk 70 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.182753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.160437 restraints weight = 9381.088| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 2.26 r_work: 0.3994 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3871 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6601 Z= 0.223 Angle : 0.564 6.690 8972 Z= 0.290 Chirality : 0.043 0.244 926 Planarity : 0.004 0.040 1163 Dihedral : 4.871 47.287 868 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.02 % Allowed : 19.86 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.50 (0.29), residues: 783 helix: 0.20 (0.27), residues: 367 sheet: -1.59 (1.16), residues: 23 loop : -0.68 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 163 HIS 0.007 0.001 HIS A 241 PHE 0.018 0.001 PHE A 523 TYR 0.022 0.002 TYR A 385 ARG 0.003 0.000 ARG A 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1894.94 seconds wall clock time: 34 minutes 9.65 seconds (2049.65 seconds total)