Starting phenix.real_space_refine on Sat Aug 3 07:41:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbx_37426/08_2024/8wbx_37426.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbx_37426/08_2024/8wbx_37426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbx_37426/08_2024/8wbx_37426.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbx_37426/08_2024/8wbx_37426.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbx_37426/08_2024/8wbx_37426.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbx_37426/08_2024/8wbx_37426.cif" } resolution = 3.23 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= -0.002 sd= 0.052 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 44 5.16 5 C 4809 2.51 5 N 1202 2.21 5 O 1276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A ASP 314": "OD1" <-> "OD2" Residue "A PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 469": "OE1" <-> "OE2" Residue "A PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 407": "OD1" <-> "OD2" Residue "B TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 432": "OD1" <-> "OD2" Residue "B PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 462": "OE1" <-> "OE2" Residue "B TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7331 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3656 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 16, 'TRANS': 450} Chain breaks: 3 Chain: "B" Number of atoms: 3656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3656 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 16, 'TRANS': 450} Chain breaks: 3 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'A8S': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.81, per 1000 atoms: 0.66 Number of scatterers: 7331 At special positions: 0 Unit cell: (80.3, 94.6, 116.6, 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 44 16.00 O 1276 8.00 N 1202 7.00 C 4809 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 - 3.50 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: 2.77 Conformation dependent library (CDL) restraints added in 1.8 seconds 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1724 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 2 sheets defined 69.8% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 106 through 111 Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'A' and resid 156 through 169 removed outlier: 3.572A pdb=" N LEU A 161 " --> pdb=" O VAL A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 208 through 222 removed outlier: 3.671A pdb=" N GLU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 256 Processing helix chain 'A' and resid 268 through 273 Processing helix chain 'A' and resid 291 through 303 removed outlier: 4.333A pdb=" N MET A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 320 Processing helix chain 'A' and resid 380 through 404 removed outlier: 3.917A pdb=" N LYS A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N HIS A 403 " --> pdb=" O LYS A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 4.207A pdb=" N GLN A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 472 removed outlier: 3.678A pdb=" N ARG A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Proline residue: A 451 - end of helix removed outlier: 3.810A pdb=" N PHE A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR A 458 " --> pdb=" O ASN A 454 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Proline residue: A 460 - end of helix removed outlier: 4.509A pdb=" N ALA A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ILE A 465 " --> pdb=" O GLN A 461 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 492 Processing helix chain 'A' and resid 493 through 508 removed outlier: 3.691A pdb=" N TRP A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 541 Processing helix chain 'A' and resid 543 through 561 Processing helix chain 'A' and resid 573 through 579 Processing helix chain 'A' and resid 581 through 594 Processing helix chain 'A' and resid 625 through 630 Processing helix chain 'A' and resid 634 through 660 removed outlier: 3.794A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 111 Processing helix chain 'B' and resid 137 through 141 Processing helix chain 'B' and resid 156 through 169 Processing helix chain 'B' and resid 174 through 189 Processing helix chain 'B' and resid 208 through 222 removed outlier: 3.671A pdb=" N GLU B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 256 Processing helix chain 'B' and resid 268 through 273 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 311 through 320 Processing helix chain 'B' and resid 380 through 406 removed outlier: 4.125A pdb=" N LYS B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU B 400 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HIS B 403 " --> pdb=" O LYS B 399 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 Processing helix chain 'B' and resid 432 through 472 removed outlier: 3.705A pdb=" N ARG B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Proline residue: B 451 - end of helix removed outlier: 3.907A pdb=" N PHE B 457 " --> pdb=" O PHE B 453 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N THR B 458 " --> pdb=" O ASN B 454 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHE B 459 " --> pdb=" O ALA B 455 " (cutoff:3.500A) Proline residue: B 460 - end of helix removed outlier: 4.547A pdb=" N ALA B 464 " --> pdb=" O PRO B 460 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ILE B 465 " --> pdb=" O GLN B 461 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 508 removed outlier: 4.076A pdb=" N SER B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 512 through 541 Processing helix chain 'B' and resid 543 through 560 Processing helix chain 'B' and resid 570 through 579 removed outlier: 3.833A pdb=" N VAL B 574 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N TRP B 575 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 595 removed outlier: 3.638A pdb=" N TYR B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 634 through 660 removed outlier: 3.591A pdb=" N ILE B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 145 removed outlier: 6.260A pdb=" N LEU A 228 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N SER A 263 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU A 230 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N MET A 97 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE A 264 " --> pdb=" O MET A 97 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL A 99 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 290 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 288 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N SER A 282 " --> pdb=" O CYS A 286 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N CYS A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.146A pdb=" N LEU B 228 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N SER B 263 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU B 230 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE B 96 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU B 279 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA B 98 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LEU B 281 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU B 100 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE B 288 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N SER B 282 " --> pdb=" O CYS B 286 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N CYS B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1371 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: 2.04 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1991 1.34 - 1.45: 1304 1.45 - 1.57: 4124 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 7495 Sorted by residual: bond pdb=" N PRO A 460 " pdb=" CD PRO A 460 " ideal model delta sigma weight residual 1.473 1.536 -0.063 1.40e-02 5.10e+03 1.99e+01 bond pdb=" N TYR B 504 " pdb=" CA TYR B 504 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.19e-02 7.06e+03 6.89e+00 bond pdb=" N LEU A 280 " pdb=" CA LEU A 280 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.19e-02 7.06e+03 6.06e+00 bond pdb=" N PHE A 275 " pdb=" CA PHE A 275 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.29e-02 6.01e+03 6.01e+00 bond pdb=" N GLN B 593 " pdb=" CA GLN B 593 " ideal model delta sigma weight residual 1.458 1.489 -0.032 1.30e-02 5.92e+03 5.90e+00 ... (remaining 7490 not shown) Histogram of bond angle deviations from ideal: 98.50 - 105.64: 142 105.64 - 112.78: 4056 112.78 - 119.92: 2476 119.92 - 127.06: 3409 127.06 - 134.20: 82 Bond angle restraints: 10165 Sorted by residual: angle pdb=" N PHE B 583 " pdb=" CA PHE B 583 " pdb=" C PHE B 583 " ideal model delta sigma weight residual 110.97 105.67 5.30 1.09e+00 8.42e-01 2.37e+01 angle pdb=" N PHE B 315 " pdb=" CA PHE B 315 " pdb=" C PHE B 315 " ideal model delta sigma weight residual 111.36 106.34 5.02 1.09e+00 8.42e-01 2.12e+01 angle pdb=" C ASP B 314 " pdb=" N PHE B 315 " pdb=" CA PHE B 315 " ideal model delta sigma weight residual 120.29 114.12 6.17 1.42e+00 4.96e-01 1.89e+01 angle pdb=" CA GLU B 159 " pdb=" CB GLU B 159 " pdb=" CG GLU B 159 " ideal model delta sigma weight residual 114.10 121.29 -7.19 2.00e+00 2.50e-01 1.29e+01 angle pdb=" O PHE B 583 " pdb=" C PHE B 583 " pdb=" N TYR B 584 " ideal model delta sigma weight residual 122.03 125.37 -3.34 1.04e+00 9.25e-01 1.03e+01 ... (remaining 10160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.41: 3966 22.41 - 44.82: 377 44.82 - 67.23: 46 67.23 - 89.64: 3 89.64 - 112.04: 10 Dihedral angle restraints: 4402 sinusoidal: 1720 harmonic: 2682 Sorted by residual: dihedral pdb=" C10 A8S A 701 " pdb=" C11 A8S A 701 " pdb=" C12 A8S A 701 " pdb=" C7 A8S A 701 " ideal model delta sinusoidal sigma weight residual 55.84 -56.20 112.04 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C15 A8S A 701 " pdb=" C12 A8S A 701 " pdb=" C7 A8S A 701 " pdb=" C5 A8S A 701 " ideal model delta sinusoidal sigma weight residual -49.34 58.90 -108.24 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" C11 A8S A 701 " pdb=" C12 A8S A 701 " pdb=" C7 A8S A 701 " pdb=" C5 A8S A 701 " ideal model delta sinusoidal sigma weight residual -169.52 -62.40 -107.12 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 4399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 954 0.047 - 0.095: 196 0.095 - 0.142: 43 0.142 - 0.189: 4 0.189 - 0.236: 2 Chirality restraints: 1199 Sorted by residual: chirality pdb=" CA PHE B 583 " pdb=" N PHE B 583 " pdb=" C PHE B 583 " pdb=" CB PHE B 583 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ILE A 660 " pdb=" N ILE A 660 " pdb=" C ILE A 660 " pdb=" CB ILE A 660 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.96e-01 chirality pdb=" CA LEU A 652 " pdb=" N LEU A 652 " pdb=" C LEU A 652 " pdb=" CB LEU A 652 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.49e-01 ... (remaining 1196 not shown) Planarity restraints: 1242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 92 " -0.040 5.00e-02 4.00e+02 6.07e-02 5.89e+00 pdb=" N PRO A 93 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 582 " 0.010 2.00e-02 2.50e+03 2.15e-02 4.60e+00 pdb=" C THR B 582 " -0.037 2.00e-02 2.50e+03 pdb=" O THR B 582 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE B 583 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 232 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.96e+00 pdb=" N PRO B 233 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 233 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 233 " 0.028 5.00e-02 4.00e+02 ... (remaining 1239 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2209 2.82 - 3.34: 7366 3.34 - 3.86: 12569 3.86 - 4.38: 13998 4.38 - 4.90: 23990 Nonbonded interactions: 60132 Sorted by model distance: nonbonded pdb=" O THR B 156 " pdb=" OG1 THR B 160 " model vdw 2.305 3.040 nonbonded pdb=" N ASP B 432 " pdb=" OD1 ASP B 432 " model vdw 2.368 3.120 nonbonded pdb=" OE1 GLU B 462 " pdb=" OH TYR B 480 " model vdw 2.402 3.040 nonbonded pdb=" O LEU A 528 " pdb=" NH2 ARG A 650 " model vdw 2.410 3.120 nonbonded pdb=" O SER A 444 " pdb=" OH TYR A 526 " model vdw 2.424 3.040 ... (remaining 60127 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 90 through 660) selection = chain 'B' } 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.920 Find NCS groups from input model: 0.280 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6176 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 0.063 7495 Z= 0.186 Angle : 0.658 9.031 10165 Z= 0.351 Chirality : 0.040 0.236 1199 Planarity : 0.004 0.061 1242 Dihedral : 16.957 112.044 2678 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.38 % Allowed : 22.92 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.77 (0.29), residues: 918 helix: 2.00 (0.21), residues: 608 sheet: 0.12 (0.66), residues: 46 loop : -0.58 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 575 HIS 0.002 0.000 HIS B 219 PHE 0.015 0.001 PHE A 499 TYR 0.026 0.001 TYR B 504 ARG 0.008 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 167 time to evaluate : 0.793 Fit side-chains revert: symmetry clash REVERT: A 252 LEU cc_start: 0.7843 (mt) cc_final: 0.7549 (mp) REVERT: A 506 MET cc_start: 0.6127 (mmp) cc_final: 0.5685 (ttt) REVERT: B 97 MET cc_start: 0.5763 (ttm) cc_final: 0.5535 (ttp) REVERT: B 569 VAL cc_start: 0.7387 (t) cc_final: 0.7135 (t) REVERT: B 575 TRP cc_start: 0.7252 (p-90) cc_final: 0.6630 (t-100) outliers start: 3 outliers final: 1 residues processed: 168 average time/residue: 0.1687 time to fit residues: 39.1081 Evaluate side-chains 150 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 507 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 0.0070 chunk 53 optimal weight: 0.4980 chunk 83 optimal weight: 0.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7495 Z= 0.172 Angle : 0.584 9.454 10165 Z= 0.274 Chirality : 0.038 0.153 1199 Planarity : 0.004 0.058 1242 Dihedral : 7.934 67.653 1035 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.65 % Allowed : 21.03 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.93 (0.28), residues: 918 helix: 2.08 (0.20), residues: 616 sheet: 0.01 (0.66), residues: 48 loop : -0.44 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 575 HIS 0.003 0.001 HIS B 219 PHE 0.022 0.001 PHE A 275 TYR 0.011 0.001 TYR B 298 ARG 0.003 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 165 time to evaluate : 0.786 Fit side-chains REVERT: A 252 LEU cc_start: 0.7805 (mt) cc_final: 0.7525 (mp) REVERT: A 310 MET cc_start: 0.8142 (ppp) cc_final: 0.7812 (ppp) REVERT: A 390 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6693 (tt) REVERT: A 555 MET cc_start: 0.6448 (tpt) cc_final: 0.6201 (tpt) REVERT: A 568 LYS cc_start: 0.7973 (tttt) cc_final: 0.7625 (tttt) REVERT: A 652 LEU cc_start: 0.8294 (mm) cc_final: 0.7896 (tp) REVERT: B 161 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7069 (mm) REVERT: B 390 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6692 (tt) REVERT: B 508 TYR cc_start: 0.5885 (t80) cc_final: 0.5680 (t80) REVERT: B 652 LEU cc_start: 0.8424 (mm) cc_final: 0.8016 (tp) outliers start: 29 outliers final: 16 residues processed: 180 average time/residue: 0.1749 time to fit residues: 43.3934 Evaluate side-chains 172 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 153 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 646 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 74 optimal weight: 0.0770 chunk 82 optimal weight: 0.9980 chunk 28 optimal weight: 0.0970 chunk 67 optimal weight: 0.7980 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7495 Z= 0.153 Angle : 0.538 8.545 10165 Z= 0.253 Chirality : 0.037 0.142 1199 Planarity : 0.004 0.049 1242 Dihedral : 5.522 50.949 1034 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.16 % Allowed : 21.66 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.87 (0.28), residues: 918 helix: 2.04 (0.20), residues: 624 sheet: -0.09 (0.64), residues: 48 loop : -0.54 (0.44), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 575 HIS 0.004 0.001 HIS B 219 PHE 0.022 0.001 PHE A 275 TYR 0.011 0.001 TYR A 475 ARG 0.009 0.000 ARG A 410 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 158 time to evaluate : 0.790 Fit side-chains REVERT: A 252 LEU cc_start: 0.7779 (mt) cc_final: 0.7484 (mp) REVERT: A 310 MET cc_start: 0.8128 (ppp) cc_final: 0.7871 (ppp) REVERT: A 390 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6718 (tt) REVERT: A 568 LYS cc_start: 0.7940 (tttt) cc_final: 0.7618 (tttt) REVERT: A 652 LEU cc_start: 0.8372 (mm) cc_final: 0.7929 (tt) REVERT: B 161 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7130 (mm) REVERT: B 275 PHE cc_start: 0.6985 (m-80) cc_final: 0.6679 (m-80) REVERT: B 310 MET cc_start: 0.8256 (ppp) cc_final: 0.7928 (ppp) REVERT: B 390 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6681 (tt) REVERT: B 462 GLU cc_start: 0.6872 (mm-30) cc_final: 0.6619 (mt-10) REVERT: B 506 MET cc_start: 0.6639 (mmp) cc_final: 0.6157 (ttt) REVERT: B 652 LEU cc_start: 0.8385 (mm) cc_final: 0.7941 (tp) outliers start: 33 outliers final: 22 residues processed: 175 average time/residue: 0.1616 time to fit residues: 39.8114 Evaluate side-chains 172 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 0.4980 chunk 56 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 74 optimal weight: 0.1980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7495 Z= 0.174 Angle : 0.539 8.765 10165 Z= 0.254 Chirality : 0.037 0.155 1199 Planarity : 0.004 0.046 1242 Dihedral : 4.605 52.107 1034 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.41 % Allowed : 22.42 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.81 (0.28), residues: 918 helix: 2.03 (0.20), residues: 614 sheet: -0.40 (0.63), residues: 48 loop : -0.50 (0.43), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 575 HIS 0.004 0.001 HIS B 219 PHE 0.025 0.002 PHE A 275 TYR 0.013 0.001 TYR B 475 ARG 0.005 0.000 ARG A 410 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 162 time to evaluate : 0.725 Fit side-chains REVERT: A 273 GLN cc_start: 0.5970 (pp30) cc_final: 0.5713 (tp40) REVERT: A 310 MET cc_start: 0.8231 (ppp) cc_final: 0.7972 (ppp) REVERT: A 390 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6724 (tt) REVERT: A 568 LYS cc_start: 0.7930 (tttt) cc_final: 0.7550 (tttt) REVERT: A 652 LEU cc_start: 0.8404 (mm) cc_final: 0.7910 (tt) REVERT: B 161 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7195 (mm) REVERT: B 273 GLN cc_start: 0.5795 (pp30) cc_final: 0.5345 (tp40) REVERT: B 275 PHE cc_start: 0.7146 (m-80) cc_final: 0.6905 (m-80) REVERT: B 310 MET cc_start: 0.8320 (ppp) cc_final: 0.7847 (ppp) REVERT: B 390 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6701 (tt) REVERT: B 506 MET cc_start: 0.6924 (mmp) cc_final: 0.6240 (ttt) REVERT: B 575 TRP cc_start: 0.7387 (p-90) cc_final: 0.6596 (t-100) outliers start: 35 outliers final: 24 residues processed: 184 average time/residue: 0.1626 time to fit residues: 42.1308 Evaluate side-chains 181 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 154 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7495 Z= 0.226 Angle : 0.584 8.769 10165 Z= 0.277 Chirality : 0.039 0.125 1199 Planarity : 0.004 0.045 1242 Dihedral : 4.519 54.951 1034 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.66 % Allowed : 23.68 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.46 (0.28), residues: 918 helix: 1.76 (0.20), residues: 612 sheet: -0.81 (0.62), residues: 48 loop : -0.52 (0.43), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 575 HIS 0.004 0.001 HIS A 219 PHE 0.022 0.002 PHE A 275 TYR 0.014 0.001 TYR B 475 ARG 0.006 0.000 ARG A 410 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 158 time to evaluate : 0.953 Fit side-chains REVERT: A 310 MET cc_start: 0.8320 (ppp) cc_final: 0.8006 (ppp) REVERT: A 555 MET cc_start: 0.6767 (tpt) cc_final: 0.6490 (tpt) REVERT: A 652 LEU cc_start: 0.8418 (mm) cc_final: 0.7911 (tt) REVERT: B 161 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7257 (mm) REVERT: B 310 MET cc_start: 0.8456 (ppp) cc_final: 0.8221 (ppp) REVERT: B 462 GLU cc_start: 0.6790 (mm-30) cc_final: 0.6479 (mt-10) REVERT: B 568 LYS cc_start: 0.7782 (tttt) cc_final: 0.7468 (tttt) REVERT: B 652 LEU cc_start: 0.8330 (mm) cc_final: 0.7970 (tp) outliers start: 37 outliers final: 31 residues processed: 179 average time/residue: 0.1648 time to fit residues: 41.1074 Evaluate side-chains 181 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 149 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 MET Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 21 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7495 Z= 0.188 Angle : 0.558 8.450 10165 Z= 0.261 Chirality : 0.038 0.125 1199 Planarity : 0.004 0.046 1242 Dihedral : 4.311 56.963 1034 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.90 % Allowed : 24.94 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.54 (0.28), residues: 918 helix: 1.82 (0.20), residues: 614 sheet: -0.99 (0.61), residues: 48 loop : -0.48 (0.42), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 575 HIS 0.004 0.001 HIS B 219 PHE 0.023 0.002 PHE A 275 TYR 0.010 0.001 TYR B 504 ARG 0.005 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 156 time to evaluate : 0.853 Fit side-chains REVERT: A 310 MET cc_start: 0.8360 (ppp) cc_final: 0.8028 (ppp) REVERT: A 506 MET cc_start: 0.6120 (mmp) cc_final: 0.5517 (ttt) REVERT: A 555 MET cc_start: 0.6913 (tpt) cc_final: 0.6669 (tpt) REVERT: A 568 LYS cc_start: 0.7973 (tttt) cc_final: 0.7626 (tttt) REVERT: A 652 LEU cc_start: 0.8397 (mm) cc_final: 0.7890 (tt) REVERT: B 161 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7212 (mm) REVERT: B 310 MET cc_start: 0.8464 (ppp) cc_final: 0.8198 (ppp) REVERT: B 398 LEU cc_start: 0.7459 (mt) cc_final: 0.7153 (mt) REVERT: B 462 GLU cc_start: 0.6741 (mm-30) cc_final: 0.6405 (mt-10) REVERT: B 506 MET cc_start: 0.6444 (mmp) cc_final: 0.5919 (ttt) REVERT: B 568 LYS cc_start: 0.7878 (tttt) cc_final: 0.7639 (tttt) REVERT: B 652 LEU cc_start: 0.8323 (mm) cc_final: 0.7817 (tp) outliers start: 31 outliers final: 24 residues processed: 174 average time/residue: 0.1699 time to fit residues: 41.0655 Evaluate side-chains 175 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 150 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 49 optimal weight: 0.0870 chunk 88 optimal weight: 0.9990 chunk 55 optimal weight: 0.0770 chunk 54 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7495 Z= 0.158 Angle : 0.555 9.895 10165 Z= 0.254 Chirality : 0.037 0.127 1199 Planarity : 0.004 0.046 1242 Dihedral : 4.192 58.892 1034 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.03 % Allowed : 25.06 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.62 (0.28), residues: 918 helix: 1.91 (0.20), residues: 614 sheet: -1.12 (0.63), residues: 46 loop : -0.51 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 575 HIS 0.003 0.001 HIS A 219 PHE 0.021 0.001 PHE A 275 TYR 0.011 0.001 TYR B 504 ARG 0.007 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 152 time to evaluate : 0.759 Fit side-chains REVERT: A 161 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7441 (mm) REVERT: A 310 MET cc_start: 0.8419 (ppp) cc_final: 0.8084 (ppp) REVERT: A 506 MET cc_start: 0.6310 (mmp) cc_final: 0.5626 (ttt) REVERT: A 555 MET cc_start: 0.6902 (tpt) cc_final: 0.6669 (tpt) REVERT: A 568 LYS cc_start: 0.7957 (tttt) cc_final: 0.7583 (tttt) REVERT: A 652 LEU cc_start: 0.8252 (mm) cc_final: 0.7870 (tt) REVERT: B 161 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7212 (mm) REVERT: B 310 MET cc_start: 0.8403 (ppp) cc_final: 0.8109 (ppp) REVERT: B 398 LEU cc_start: 0.7431 (mt) cc_final: 0.7119 (mt) REVERT: B 462 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6476 (mt-10) REVERT: B 506 MET cc_start: 0.6770 (mmp) cc_final: 0.6246 (ttt) REVERT: B 652 LEU cc_start: 0.8309 (mm) cc_final: 0.7814 (tp) outliers start: 32 outliers final: 23 residues processed: 171 average time/residue: 0.1734 time to fit residues: 40.6462 Evaluate side-chains 170 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 145 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 80 optimal weight: 0.4980 chunk 84 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7495 Z= 0.176 Angle : 0.565 9.318 10165 Z= 0.260 Chirality : 0.038 0.124 1199 Planarity : 0.004 0.051 1242 Dihedral : 4.156 59.300 1034 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.90 % Allowed : 24.81 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.61 (0.28), residues: 918 helix: 1.95 (0.20), residues: 612 sheet: -1.26 (0.63), residues: 46 loop : -0.57 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 575 HIS 0.003 0.001 HIS A 219 PHE 0.019 0.001 PHE A 275 TYR 0.011 0.001 TYR A 475 ARG 0.007 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 152 time to evaluate : 0.838 Fit side-chains REVERT: A 159 GLU cc_start: 0.6838 (mm-30) cc_final: 0.6439 (tp30) REVERT: A 161 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7423 (mm) REVERT: A 310 MET cc_start: 0.8454 (ppp) cc_final: 0.8108 (ppp) REVERT: A 506 MET cc_start: 0.6349 (mmp) cc_final: 0.5651 (ttt) REVERT: A 555 MET cc_start: 0.6935 (tpt) cc_final: 0.6730 (tpt) REVERT: A 568 LYS cc_start: 0.7971 (tttt) cc_final: 0.7578 (tttt) REVERT: A 652 LEU cc_start: 0.8229 (mm) cc_final: 0.7900 (tt) REVERT: B 161 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7244 (mm) REVERT: B 310 MET cc_start: 0.8467 (ppp) cc_final: 0.8184 (ppp) REVERT: B 398 LEU cc_start: 0.7438 (mt) cc_final: 0.7129 (mt) REVERT: B 462 GLU cc_start: 0.6834 (mm-30) cc_final: 0.6525 (mt-10) REVERT: B 506 MET cc_start: 0.6761 (mmp) cc_final: 0.6197 (ttt) REVERT: B 575 TRP cc_start: 0.7423 (p-90) cc_final: 0.6399 (t-100) REVERT: B 635 MET cc_start: 0.6920 (mmm) cc_final: 0.6596 (tpp) REVERT: B 652 LEU cc_start: 0.8332 (mm) cc_final: 0.7809 (tp) outliers start: 31 outliers final: 25 residues processed: 170 average time/residue: 0.1736 time to fit residues: 40.8396 Evaluate side-chains 173 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 146 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 646 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 0.2980 chunk 82 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 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 247 GLN ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7495 Z= 0.178 Angle : 0.590 9.007 10165 Z= 0.273 Chirality : 0.038 0.130 1199 Planarity : 0.004 0.053 1242 Dihedral : 4.165 59.896 1034 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.78 % Allowed : 25.94 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.56 (0.28), residues: 918 helix: 1.95 (0.20), residues: 610 sheet: -1.32 (0.63), residues: 46 loop : -0.66 (0.41), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 575 HIS 0.003 0.001 HIS A 219 PHE 0.017 0.001 PHE B 275 TYR 0.010 0.001 TYR A 475 ARG 0.008 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 149 time to evaluate : 0.792 Fit side-chains REVERT: A 159 GLU cc_start: 0.6814 (mm-30) cc_final: 0.6404 (tp30) REVERT: A 161 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7395 (mm) REVERT: A 310 MET cc_start: 0.8461 (ppp) cc_final: 0.8117 (ppp) REVERT: A 568 LYS cc_start: 0.7994 (tttt) cc_final: 0.7692 (tttt) REVERT: A 652 LEU cc_start: 0.8316 (mm) cc_final: 0.7897 (tt) REVERT: B 161 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7178 (mm) REVERT: B 310 MET cc_start: 0.8392 (ppp) cc_final: 0.8094 (ppp) REVERT: B 398 LEU cc_start: 0.7427 (mt) cc_final: 0.7118 (mt) REVERT: B 462 GLU cc_start: 0.6829 (mm-30) cc_final: 0.6514 (mt-10) REVERT: B 502 PHE cc_start: 0.6534 (t80) cc_final: 0.6255 (t80) REVERT: B 506 MET cc_start: 0.6828 (mmp) cc_final: 0.6097 (ttt) REVERT: B 598 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7242 (mp0) REVERT: B 635 MET cc_start: 0.6946 (mmm) cc_final: 0.6644 (tpp) REVERT: B 652 LEU cc_start: 0.8325 (mm) cc_final: 0.7807 (tp) outliers start: 30 outliers final: 26 residues processed: 167 average time/residue: 0.1737 time to fit residues: 39.8048 Evaluate side-chains 173 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 145 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 646 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 57 optimal weight: 0.0570 chunk 77 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7495 Z= 0.184 Angle : 0.597 8.831 10165 Z= 0.277 Chirality : 0.038 0.122 1199 Planarity : 0.004 0.055 1242 Dihedral : 4.140 59.340 1034 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.90 % Allowed : 25.57 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.54 (0.28), residues: 918 helix: 1.93 (0.21), residues: 610 sheet: -1.42 (0.64), residues: 46 loop : -0.65 (0.41), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 575 HIS 0.003 0.001 HIS A 219 PHE 0.016 0.001 PHE B 275 TYR 0.010 0.001 TYR A 475 ARG 0.009 0.001 ARG B 205 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 146 time to evaluate : 0.749 Fit side-chains REVERT: A 159 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6488 (tp30) REVERT: A 161 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7370 (mm) REVERT: A 310 MET cc_start: 0.8462 (ppp) cc_final: 0.8114 (ppp) REVERT: A 506 MET cc_start: 0.6036 (mmp) cc_final: 0.5638 (ttt) REVERT: A 635 MET cc_start: 0.6772 (tpp) cc_final: 0.6401 (tpt) REVERT: A 652 LEU cc_start: 0.8231 (mm) cc_final: 0.7918 (tt) REVERT: B 161 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7173 (mm) REVERT: B 310 MET cc_start: 0.8266 (ppp) cc_final: 0.7925 (ppp) REVERT: B 398 LEU cc_start: 0.7426 (mt) cc_final: 0.7110 (mt) REVERT: B 402 ARG cc_start: 0.6238 (OUTLIER) cc_final: 0.5459 (ptm-80) REVERT: B 462 GLU cc_start: 0.6829 (mm-30) cc_final: 0.6518 (mt-10) REVERT: B 502 PHE cc_start: 0.6537 (t80) cc_final: 0.6255 (t80) REVERT: B 506 MET cc_start: 0.6810 (mmp) cc_final: 0.6127 (ttt) REVERT: B 598 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7130 (mp0) REVERT: B 635 MET cc_start: 0.6994 (mmm) cc_final: 0.6737 (tpp) REVERT: B 652 LEU cc_start: 0.8326 (mm) cc_final: 0.7823 (tp) outliers start: 31 outliers final: 26 residues processed: 164 average time/residue: 0.1844 time to fit residues: 41.5905 Evaluate side-chains 171 residues out of total 794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 142 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 430 TYR Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 504 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 430 TYR Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 580 SER Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 646 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 GLN ** B 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.174431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.148462 restraints weight = 10114.975| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 2.90 r_work: 0.4012 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7495 Z= 0.210 Angle : 0.610 8.629 10165 Z= 0.285 Chirality : 0.038 0.145 1199 Planarity : 0.005 0.060 1242 Dihedral : 4.181 59.086 1034 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.28 % Allowed : 24.81 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.42 (0.28), residues: 918 helix: 1.85 (0.21), residues: 610 sheet: -1.61 (0.64), residues: 46 loop : -0.68 (0.41), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 575 HIS 0.003 0.001 HIS B 219 PHE 0.020 0.002 PHE A 163 TYR 0.011 0.001 TYR A 475 ARG 0.008 0.001 ARG B 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1835.90 seconds wall clock time: 33 minutes 22.23 seconds (2002.23 seconds total)