Starting phenix.real_space_refine on Fri Jan 19 06:01:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r89_24312/01_2024/7r89_24312_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r89_24312/01_2024/7r89_24312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r89_24312/01_2024/7r89_24312.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r89_24312/01_2024/7r89_24312.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r89_24312/01_2024/7r89_24312_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r89_24312/01_2024/7r89_24312_updated.pdb" } resolution = 2.6 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 ------------------------------------------------------------------------------- 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= 0.002 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 66 5.16 5 C 6811 2.51 5 N 1778 2.21 5 O 1876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 77": "OE1" <-> "OE2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 579": "OE1" <-> "OE2" Residue "B PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B GLU 189": "OE1" <-> "OE2" Residue "B ARG 257": "NH1" <-> "NH2" Residue "B GLU 481": "OE1" <-> "OE2" Residue "B GLU 483": "OE1" <-> "OE2" Residue "B GLU 503": "OE1" <-> "OE2" Residue "B GLU 634": "OE1" <-> "OE2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "C ARG 108": "NH1" <-> "NH2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "D GLU 125": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 10531 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4596 Classifications: {'peptide': 584} Link IDs: {'PTRANS': 22, 'TRANS': 561} Chain breaks: 3 Chain: "B" Number of atoms: 4202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4202 Classifications: {'peptide': 529} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 504} Chain breaks: 5 Chain: "C" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 901 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "D" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 803 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 100} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'ERG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.83, per 1000 atoms: 0.55 Number of scatterers: 10531 At special positions: 0 Unit cell: (116.48, 101.504, 123.968, 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 66 16.00 O 1876 8.00 N 1778 7.00 C 6811 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 587 " - pdb=" SG CYS A 600 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 117 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 108 " 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: 4.07 Conformation dependent library (CDL) restraints added in 1.9 seconds 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2468 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 9 sheets defined 47.1% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'A' and resid 92 through 100 Processing helix chain 'A' and resid 144 through 155 Processing helix chain 'A' and resid 161 through 174 Processing helix chain 'A' and resid 195 through 209 removed outlier: 4.604A pdb=" N GLN A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 240 Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 277 through 286 Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 312 through 330 Processing helix chain 'A' and resid 333 through 346 Processing helix chain 'A' and resid 364 through 380 Processing helix chain 'A' and resid 383 through 404 removed outlier: 5.475A pdb=" N ASN A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LEU A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE A 403 " --> pdb=" O PHE A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 453 Proline residue: A 431 - end of helix Proline residue: A 443 - end of helix Processing helix chain 'A' and resid 460 through 490 Proline residue: A 473 - end of helix removed outlier: 4.993A pdb=" N TRP A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 523 Proline residue: A 509 - end of helix Processing helix chain 'A' and resid 527 through 544 Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'A' and resid 557 through 565 removed outlier: 3.638A pdb=" N TYR A 564 " --> pdb=" O LYS A 560 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 579 Processing helix chain 'A' and resid 605 through 612 Processing helix chain 'A' and resid 617 through 648 removed outlier: 4.156A pdb=" N PHE A 620 " --> pdb=" O THR A 617 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N THR A 621 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET A 622 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE A 631 " --> pdb=" O TYR A 628 " (cutoff:3.500A) Proline residue: A 632 - end of helix Processing helix chain 'B' and resid 114 through 119 Processing helix chain 'B' and resid 141 through 147 removed outlier: 3.730A pdb=" N ARG B 145 " --> pdb=" O PRO B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 174 Processing helix chain 'B' and resid 181 through 194 Processing helix chain 'B' and resid 215 through 225 Processing helix chain 'B' and resid 245 through 259 Processing helix chain 'B' and resid 277 through 279 No H-bonds generated for 'chain 'B' and resid 277 through 279' Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 317 through 323 Processing helix chain 'B' and resid 395 through 410 Processing helix chain 'B' and resid 414 through 434 Processing helix chain 'B' and resid 445 through 472 removed outlier: 4.638A pdb=" N ILE B 459 " --> pdb=" O ILE B 455 " (cutoff:3.500A) Proline residue: B 460 - end of helix Processing helix chain 'B' and resid 475 through 484 Processing helix chain 'B' and resid 491 through 516 Proline residue: B 502 - end of helix Proline residue: B 514 - end of helix Processing helix chain 'B' and resid 526 through 552 Processing helix chain 'B' and resid 556 through 572 Processing helix chain 'B' and resid 586 through 592 Processing helix chain 'B' and resid 595 through 608 Processing helix chain 'B' and resid 627 through 632 Processing helix chain 'B' and resid 640 through 664 Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'D' and resid 100 through 102 No H-bonds generated for 'chain 'D' and resid 100 through 102' Processing sheet with id= A, first strand: chain 'A' and resid 74 through 77 Processing sheet with id= B, first strand: chain 'A' and resid 270 through 275 removed outlier: 6.576A pdb=" N ILE A 265 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N CYS A 274 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE A 263 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL A 245 " --> pdb=" O MET A 82 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE A 84 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU A 247 " --> pdb=" O ILE A 84 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N GLY A 86 " --> pdb=" O LEU A 247 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 93 through 96 Processing sheet with id= D, first strand: chain 'B' and resid 290 through 296 removed outlier: 6.772A pdb=" N LEU B 285 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU B 294 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL B 283 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL B 265 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE B 103 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE B 267 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N GLY B 105 " --> pdb=" O ILE B 267 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 22 through 26 Processing sheet with id= F, first strand: chain 'C' and resid 116 through 118 removed outlier: 6.105A pdb=" N ARG C 57 " --> pdb=" O TRP C 66 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N TRP C 66 " --> pdb=" O ARG C 57 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 24 through 27 Processing sheet with id= H, first strand: chain 'D' and resid 30 through 32 removed outlier: 5.958A pdb=" N LYS D 123 " --> pdb=" O LEU D 31 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'D' and resid 104 through 110 removed outlier: 6.279A pdb=" N GLN D 57 " --> pdb=" O ARG D 66 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ARG D 66 " --> pdb=" O GLN D 57 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS D 59 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE D 64 " --> pdb=" O LYS D 59 " (cutoff:3.500A) 519 hydrogen bonds defined for protein. 1449 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: 3.09 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3342 1.35 - 1.46: 2562 1.46 - 1.58: 4752 1.58 - 1.70: 0 1.70 - 1.82: 105 Bond restraints: 10761 Sorted by residual: bond pdb=" C10 ERG B 901 " pdb=" C9 ERG B 901 " ideal model delta sigma weight residual 1.556 1.507 0.049 2.00e-02 2.50e+03 6.12e+00 bond pdb=" N ARG C 63 " pdb=" CA ARG C 63 " ideal model delta sigma weight residual 1.459 1.473 -0.015 1.16e-02 7.43e+03 1.61e+00 bond pdb=" C10 ERG B 901 " pdb=" C5 ERG B 901 " ideal model delta sigma weight residual 1.519 1.496 0.023 2.00e-02 2.50e+03 1.37e+00 bond pdb=" N THR B 489 " pdb=" CA THR B 489 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.15e+00 bond pdb=" C ILE B 459 " pdb=" N PRO B 460 " ideal model delta sigma weight residual 1.335 1.348 -0.014 1.28e-02 6.10e+03 1.14e+00 ... (remaining 10756 not shown) Histogram of bond angle deviations from ideal: 100.17 - 106.93: 298 106.93 - 113.69: 5850 113.69 - 120.45: 4271 120.45 - 127.22: 4056 127.22 - 133.98: 96 Bond angle restraints: 14571 Sorted by residual: angle pdb=" C PRO A 556 " pdb=" N ILE A 557 " pdb=" CA ILE A 557 " ideal model delta sigma weight residual 120.33 123.30 -2.97 8.00e-01 1.56e+00 1.38e+01 angle pdb=" N VAL B 205 " pdb=" CA VAL B 205 " pdb=" CB VAL B 205 " ideal model delta sigma weight residual 112.39 108.80 3.59 1.17e+00 7.31e-01 9.42e+00 angle pdb=" C ARG C 63 " pdb=" CA ARG C 63 " pdb=" CB ARG C 63 " ideal model delta sigma weight residual 110.92 115.60 -4.68 1.59e+00 3.96e-01 8.66e+00 angle pdb=" C THR B 488 " pdb=" N THR B 489 " pdb=" CA THR B 489 " ideal model delta sigma weight residual 121.54 127.03 -5.49 1.91e+00 2.74e-01 8.27e+00 angle pdb=" N ILE B 459 " pdb=" CA ILE B 459 " pdb=" C ILE B 459 " ideal model delta sigma weight residual 108.88 115.05 -6.17 2.16e+00 2.14e-01 8.16e+00 ... (remaining 14566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 5818 17.96 - 35.91: 460 35.91 - 53.86: 133 53.86 - 71.82: 30 71.82 - 89.77: 11 Dihedral angle restraints: 6452 sinusoidal: 2608 harmonic: 3844 Sorted by residual: dihedral pdb=" CB CYS A 587 " pdb=" SG CYS A 587 " pdb=" SG CYS A 600 " pdb=" CB CYS A 600 " ideal model delta sinusoidal sigma weight residual -86.00 -159.55 73.55 1 1.00e+01 1.00e-02 6.88e+01 dihedral pdb=" CB CYS D 43 " pdb=" SG CYS D 43 " pdb=" SG CYS D 108 " pdb=" CB CYS D 108 " ideal model delta sinusoidal sigma weight residual 93.00 65.05 27.95 1 1.00e+01 1.00e-02 1.12e+01 dihedral pdb=" CB GLU B 483 " pdb=" CG GLU B 483 " pdb=" CD GLU B 483 " pdb=" OE1 GLU B 483 " ideal model delta sinusoidal sigma weight residual 0.00 89.77 -89.77 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 6449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1638 0.111 - 0.222: 22 0.222 - 0.334: 0 0.334 - 0.445: 1 0.445 - 0.556: 1 Chirality restraints: 1662 Sorted by residual: chirality pdb=" C14 ERG B 901 " pdb=" C13 ERG B 901 " pdb=" C15 ERG B 901 " pdb=" C8 ERG B 901 " both_signs ideal model delta sigma weight residual False -2.26 -2.82 0.56 2.00e-01 2.50e+01 7.73e+00 chirality pdb=" C10 ERG B 901 " pdb=" C1 ERG B 901 " pdb=" C5 ERG B 901 " pdb=" C9 ERG B 901 " both_signs ideal model delta sigma weight residual False -2.77 -2.38 -0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" C13 ERG B 901 " pdb=" C12 ERG B 901 " pdb=" C14 ERG B 901 " pdb=" C17 ERG B 901 " both_signs ideal model delta sigma weight residual False -2.93 -2.71 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1659 not shown) Planarity restraints: 1828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 ERG B 901 " 0.146 2.00e-02 2.50e+03 1.47e-01 2.15e+02 pdb=" C22 ERG B 901 " -0.141 2.00e-02 2.50e+03 pdb=" C23 ERG B 901 " -0.152 2.00e-02 2.50e+03 pdb=" C24 ERG B 901 " 0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 513 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO B 514 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 514 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 514 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 276 " 0.022 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO A 277 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 277 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 277 " 0.019 5.00e-02 4.00e+02 ... (remaining 1825 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1405 2.76 - 3.29: 10159 3.29 - 3.83: 18281 3.83 - 4.36: 21142 4.36 - 4.90: 37168 Nonbonded interactions: 88155 Sorted by model distance: nonbonded pdb=" O ALA B 573 " pdb=" OG SER B 591 " model vdw 2.221 2.440 nonbonded pdb=" OG SER D 83 " pdb=" OG1 THR D 94 " model vdw 2.271 2.440 nonbonded pdb=" OG SER B 428 " pdb=" OG1 THR B 515 " model vdw 2.292 2.440 nonbonded pdb=" OG SER B 428 " pdb=" O TYR B 511 " model vdw 2.299 2.440 nonbonded pdb=" OH TYR B 293 " pdb=" O ALA B 296 " model vdw 2.312 2.440 ... (remaining 88150 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: 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: 5.810 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 30.870 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 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 : 0.002 0.049 10761 Z= 0.135 Angle : 0.561 7.876 14571 Z= 0.318 Chirality : 0.041 0.556 1662 Planarity : 0.005 0.147 1828 Dihedral : 14.779 89.774 3975 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.39 % Allowed : 16.67 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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 (0.22), residues: 1308 helix: 0.26 (0.19), residues: 681 sheet: -1.46 (0.33), residues: 178 loop : -2.63 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 55 HIS 0.003 0.001 HIS B 531 PHE 0.013 0.001 PHE B 493 TYR 0.008 0.001 TYR A 487 ARG 0.002 0.000 ARG C 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 224 time to evaluate : 1.232 Fit side-chains revert: symmetry clash REVERT: A 435 MET cc_start: 0.8706 (tmm) cc_final: 0.8408 (tmm) REVERT: B 146 LYS cc_start: 0.8680 (tmmt) cc_final: 0.8391 (tttm) REVERT: B 156 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7316 (mm-40) REVERT: B 517 TRP cc_start: 0.7264 (m100) cc_final: 0.6768 (t60) REVERT: B 577 MET cc_start: 0.6459 (OUTLIER) cc_final: 0.5841 (mtp) outliers start: 39 outliers final: 14 residues processed: 255 average time/residue: 1.2070 time to fit residues: 331.3947 Evaluate side-chains 167 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 151 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 587 CYS Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 100 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 0.0470 chunk 33 optimal weight: 4.9990 chunk 66 optimal weight: 0.0000 chunk 53 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 overall best weight: 1.2088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 378 ASN A 393 ASN A 425 GLN A 459 GLN A 462 GLN A 578 ASN B 99 GLN B 199 GLN B 249 HIS B 270 HIS B 302 GLN B 409 ASN B 438 HIS B 568 ASN C 58 GLN C 75 ASN C 103 GLN D 26 GLN D 47 GLN D 58 GLN D 65 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10761 Z= 0.241 Angle : 0.561 7.975 14571 Z= 0.284 Chirality : 0.040 0.137 1662 Planarity : 0.004 0.043 1828 Dihedral : 5.938 57.304 1549 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 5.12 % Allowed : 19.18 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.23), residues: 1308 helix: 1.17 (0.19), residues: 682 sheet: -0.94 (0.36), residues: 171 loop : -1.99 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 133 HIS 0.007 0.001 HIS B 249 PHE 0.022 0.002 PHE A 585 TYR 0.019 0.002 TYR A 628 ARG 0.006 0.001 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 147 time to evaluate : 1.224 Fit side-chains revert: symmetry clash REVERT: A 435 MET cc_start: 0.9010 (tmm) cc_final: 0.8738 (tmm) REVERT: A 647 HIS cc_start: 0.6589 (OUTLIER) cc_final: 0.6346 (t-90) REVERT: B 100 MET cc_start: 0.8816 (ttp) cc_final: 0.8575 (ttp) REVERT: B 392 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7528 (mpp) REVERT: B 483 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7781 (tt0) REVERT: B 517 TRP cc_start: 0.7419 (m100) cc_final: 0.7037 (t60) REVERT: C 103 GLN cc_start: 0.8475 (tp40) cc_final: 0.8091 (tp40) REVERT: D 90 ASP cc_start: 0.8536 (m-30) cc_final: 0.8294 (m-30) outliers start: 59 outliers final: 24 residues processed: 189 average time/residue: 1.1677 time to fit residues: 238.6775 Evaluate side-chains 166 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain A residue 647 HIS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 32 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS A 392 GLN A 425 GLN A 493 HIS B 607 GLN D 65 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10761 Z= 0.275 Angle : 0.576 10.149 14571 Z= 0.291 Chirality : 0.041 0.140 1662 Planarity : 0.004 0.045 1828 Dihedral : 5.119 59.178 1533 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.95 % Allowed : 19.70 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.23), residues: 1308 helix: 1.36 (0.20), residues: 681 sheet: -0.75 (0.36), residues: 186 loop : -1.69 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 229 HIS 0.004 0.001 HIS A 510 PHE 0.018 0.002 PHE A 642 TYR 0.016 0.002 TYR A 114 ARG 0.003 0.000 ARG B 263 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 141 time to evaluate : 1.308 Fit side-chains revert: symmetry clash REVERT: A 425 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8252 (mp-120) REVERT: B 100 MET cc_start: 0.8772 (ttp) cc_final: 0.8527 (ttp) REVERT: B 156 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7434 (mm-40) REVERT: B 483 GLU cc_start: 0.8079 (tt0) cc_final: 0.7865 (tt0) REVERT: B 503 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7690 (tt0) REVERT: B 517 TRP cc_start: 0.7402 (m100) cc_final: 0.7002 (t60) REVERT: B 582 SER cc_start: 0.7506 (OUTLIER) cc_final: 0.7252 (p) REVERT: C 99 ILE cc_start: 0.9123 (mt) cc_final: 0.8708 (mp) REVERT: C 103 GLN cc_start: 0.8499 (tp40) cc_final: 0.8089 (tp40) REVERT: C 130 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7749 (pm20) outliers start: 57 outliers final: 24 residues processed: 182 average time/residue: 1.1900 time to fit residues: 234.1656 Evaluate side-chains 160 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 131 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 116 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 607 GLN D 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10761 Z= 0.363 Angle : 0.611 10.549 14571 Z= 0.310 Chirality : 0.043 0.153 1662 Planarity : 0.005 0.048 1828 Dihedral : 5.211 55.984 1531 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 5.12 % Allowed : 20.40 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.23), residues: 1308 helix: 1.35 (0.20), residues: 680 sheet: -0.59 (0.36), residues: 186 loop : -1.53 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 584 HIS 0.004 0.001 HIS B 531 PHE 0.020 0.002 PHE C 125 TYR 0.016 0.002 TYR A 114 ARG 0.007 0.001 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 137 time to evaluate : 1.351 Fit side-chains revert: symmetry clash REVERT: B 100 MET cc_start: 0.8775 (ttp) cc_final: 0.8453 (ttp) REVERT: B 483 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7856 (tt0) REVERT: B 503 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7719 (tt0) REVERT: B 517 TRP cc_start: 0.7394 (m100) cc_final: 0.7011 (t60) REVERT: B 582 SER cc_start: 0.7567 (OUTLIER) cc_final: 0.7314 (p) REVERT: C 54 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.7601 (mm-30) REVERT: C 99 ILE cc_start: 0.9109 (mt) cc_final: 0.8694 (mp) REVERT: C 103 GLN cc_start: 0.8536 (tp40) cc_final: 0.7817 (tp-100) REVERT: C 130 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7703 (pm20) outliers start: 59 outliers final: 33 residues processed: 181 average time/residue: 1.1819 time to fit residues: 231.0821 Evaluate side-chains 166 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 128 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 116 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 64 optimal weight: 0.0570 chunk 113 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN D 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10761 Z= 0.260 Angle : 0.566 10.297 14571 Z= 0.286 Chirality : 0.041 0.137 1662 Planarity : 0.004 0.049 1828 Dihedral : 5.078 56.821 1531 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.86 % Allowed : 20.92 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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 (0.24), residues: 1308 helix: 1.51 (0.20), residues: 679 sheet: -0.47 (0.37), residues: 186 loop : -1.44 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 229 HIS 0.004 0.001 HIS A 510 PHE 0.017 0.001 PHE B 493 TYR 0.018 0.001 TYR A 114 ARG 0.005 0.000 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 132 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: A 334 ILE cc_start: 0.8091 (mm) cc_final: 0.7843 (mt) REVERT: A 425 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8030 (mp10) REVERT: B 100 MET cc_start: 0.8753 (ttp) cc_final: 0.8542 (ttp) REVERT: B 156 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7436 (mm-40) REVERT: B 483 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: B 503 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7721 (tt0) REVERT: B 517 TRP cc_start: 0.7372 (m100) cc_final: 0.6976 (t60) REVERT: B 582 SER cc_start: 0.7484 (OUTLIER) cc_final: 0.7232 (p) REVERT: C 99 ILE cc_start: 0.9126 (mt) cc_final: 0.8724 (mp) REVERT: C 103 GLN cc_start: 0.8493 (tp40) cc_final: 0.7768 (tp-100) REVERT: C 130 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7693 (pm20) outliers start: 56 outliers final: 30 residues processed: 175 average time/residue: 1.2424 time to fit residues: 235.3910 Evaluate side-chains 161 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 125 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 116 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN D 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10761 Z= 0.287 Angle : 0.586 10.469 14571 Z= 0.296 Chirality : 0.041 0.154 1662 Planarity : 0.004 0.049 1828 Dihedral : 5.116 56.178 1531 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.60 % Allowed : 20.83 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.41 (0.24), residues: 1308 helix: 1.50 (0.20), residues: 680 sheet: -0.44 (0.37), residues: 186 loop : -1.33 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 229 HIS 0.005 0.001 HIS A 510 PHE 0.018 0.002 PHE B 493 TYR 0.014 0.002 TYR A 114 ARG 0.008 0.000 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 130 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 ILE cc_start: 0.8133 (mm) cc_final: 0.7889 (mt) REVERT: A 425 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8052 (mp10) REVERT: B 26 ARG cc_start: 0.4651 (ptt180) cc_final: 0.4449 (ptt180) REVERT: B 100 MET cc_start: 0.8834 (ttp) cc_final: 0.8520 (ttp) REVERT: B 156 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7495 (mm-40) REVERT: B 483 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7845 (tt0) REVERT: B 503 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7698 (tt0) REVERT: B 517 TRP cc_start: 0.7404 (m100) cc_final: 0.6987 (t60) REVERT: B 582 SER cc_start: 0.7525 (OUTLIER) cc_final: 0.7265 (p) REVERT: C 54 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.7688 (mm-30) REVERT: C 99 ILE cc_start: 0.9134 (mt) cc_final: 0.8727 (mp) REVERT: C 103 GLN cc_start: 0.8498 (tp40) cc_final: 0.7827 (tp-100) REVERT: C 130 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7701 (pm20) outliers start: 53 outliers final: 35 residues processed: 168 average time/residue: 1.1459 time to fit residues: 208.8120 Evaluate side-chains 166 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 124 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 116 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN D 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10761 Z= 0.226 Angle : 0.566 10.175 14571 Z= 0.283 Chirality : 0.040 0.144 1662 Planarity : 0.004 0.049 1828 Dihedral : 5.013 56.224 1531 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.51 % Allowed : 21.01 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.54 (0.24), residues: 1308 helix: 1.60 (0.20), residues: 680 sheet: -0.46 (0.36), residues: 191 loop : -1.22 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 229 HIS 0.004 0.001 HIS B 531 PHE 0.017 0.001 PHE B 493 TYR 0.014 0.001 TYR A 114 ARG 0.007 0.000 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 129 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 ILE cc_start: 0.8089 (mm) cc_final: 0.7854 (mt) REVERT: A 425 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8010 (mp10) REVERT: A 529 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8803 (mp) REVERT: B 100 MET cc_start: 0.8811 (ttp) cc_final: 0.8499 (ttp) REVERT: B 156 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7506 (mm-40) REVERT: B 483 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7845 (tt0) REVERT: B 503 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7684 (tt0) REVERT: B 517 TRP cc_start: 0.7381 (m100) cc_final: 0.6968 (t60) REVERT: B 582 SER cc_start: 0.7492 (OUTLIER) cc_final: 0.7223 (p) REVERT: C 54 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.7608 (mm-30) REVERT: C 99 ILE cc_start: 0.9108 (mt) cc_final: 0.8707 (mp) REVERT: C 103 GLN cc_start: 0.8489 (tp40) cc_final: 0.7845 (tp-100) REVERT: C 130 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7691 (pm20) REVERT: D 38 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7870 (ptm-80) outliers start: 52 outliers final: 33 residues processed: 168 average time/residue: 1.1669 time to fit residues: 212.4125 Evaluate side-chains 167 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 125 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 116 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 75 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN D 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10761 Z= 0.168 Angle : 0.543 9.739 14571 Z= 0.270 Chirality : 0.039 0.143 1662 Planarity : 0.004 0.050 1828 Dihedral : 4.870 57.000 1531 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.51 % Allowed : 20.92 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.76 (0.24), residues: 1308 helix: 1.78 (0.20), residues: 678 sheet: -0.31 (0.37), residues: 188 loop : -1.14 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 229 HIS 0.004 0.001 HIS B 531 PHE 0.017 0.001 PHE B 493 TYR 0.013 0.001 TYR A 114 ARG 0.007 0.000 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 137 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 MET cc_start: 0.8242 (mmm) cc_final: 0.8037 (tpp) REVERT: A 334 ILE cc_start: 0.8086 (mm) cc_final: 0.7842 (mt) REVERT: A 425 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8011 (mp10) REVERT: A 529 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8822 (mp) REVERT: B 100 MET cc_start: 0.8781 (ttp) cc_final: 0.8561 (ttp) REVERT: B 156 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7504 (mm-40) REVERT: B 503 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7674 (tt0) REVERT: B 517 TRP cc_start: 0.7407 (m100) cc_final: 0.6986 (t60) REVERT: B 582 SER cc_start: 0.7423 (OUTLIER) cc_final: 0.7151 (p) REVERT: C 99 ILE cc_start: 0.9106 (mt) cc_final: 0.8723 (mp) REVERT: C 103 GLN cc_start: 0.8454 (tp40) cc_final: 0.7847 (tp-100) REVERT: C 130 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7688 (pm20) REVERT: D 38 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7885 (ptm-80) outliers start: 52 outliers final: 31 residues processed: 177 average time/residue: 1.1360 time to fit residues: 218.0076 Evaluate side-chains 161 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 123 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 116 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10761 Z= 0.268 Angle : 0.596 11.411 14571 Z= 0.296 Chirality : 0.042 0.266 1662 Planarity : 0.004 0.049 1828 Dihedral : 4.973 52.833 1531 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.99 % Allowed : 21.44 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.69 (0.24), residues: 1308 helix: 1.65 (0.20), residues: 682 sheet: -0.24 (0.37), residues: 186 loop : -1.10 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 584 HIS 0.004 0.001 HIS B 531 PHE 0.018 0.002 PHE B 493 TYR 0.012 0.001 TYR B 571 ARG 0.007 0.000 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 126 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 ILE cc_start: 0.8096 (mm) cc_final: 0.7853 (mt) REVERT: A 412 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7912 (tm) REVERT: A 425 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8025 (mp10) REVERT: B 100 MET cc_start: 0.8830 (ttp) cc_final: 0.8526 (ttp) REVERT: B 156 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7525 (mm-40) REVERT: B 503 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7693 (tt0) REVERT: B 517 TRP cc_start: 0.7378 (m100) cc_final: 0.6946 (t60) REVERT: B 582 SER cc_start: 0.7511 (OUTLIER) cc_final: 0.7219 (p) REVERT: C 99 ILE cc_start: 0.9121 (mt) cc_final: 0.8736 (mp) REVERT: C 103 GLN cc_start: 0.8483 (tp40) cc_final: 0.7806 (tp-100) REVERT: C 130 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7708 (pm20) outliers start: 46 outliers final: 32 residues processed: 162 average time/residue: 1.1469 time to fit residues: 201.0641 Evaluate side-chains 162 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 124 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 116 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 3.9990 chunk 59 optimal weight: 0.0270 chunk 86 optimal weight: 0.0070 chunk 130 optimal weight: 0.4980 chunk 120 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 82 optimal weight: 0.0970 chunk 110 optimal weight: 8.9990 overall best weight: 0.2454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 249 HIS B 607 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10761 Z= 0.124 Angle : 0.537 11.765 14571 Z= 0.264 Chirality : 0.039 0.204 1662 Planarity : 0.004 0.051 1828 Dihedral : 4.654 58.879 1531 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.60 % Allowed : 22.92 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 1.00 (0.24), residues: 1308 helix: 1.95 (0.20), residues: 679 sheet: -0.25 (0.37), residues: 191 loop : -0.95 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 536 HIS 0.004 0.000 HIS B 531 PHE 0.015 0.001 PHE B 493 TYR 0.013 0.001 TYR A 114 ARG 0.006 0.000 ARG D 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2616 Ramachandran restraints generated. 1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 1.197 Fit side-chains revert: symmetry clash REVERT: A 334 ILE cc_start: 0.8057 (mm) cc_final: 0.7835 (mt) REVERT: A 345 MET cc_start: 0.7805 (tpp) cc_final: 0.7477 (pp-130) REVERT: B 156 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7499 (mm-40) REVERT: B 503 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7533 (tt0) REVERT: B 517 TRP cc_start: 0.7347 (m100) cc_final: 0.6930 (t60) REVERT: B 582 SER cc_start: 0.7230 (OUTLIER) cc_final: 0.6981 (p) REVERT: C 99 ILE cc_start: 0.9115 (mt) cc_final: 0.8700 (mp) REVERT: C 103 GLN cc_start: 0.8447 (tp40) cc_final: 0.7792 (tp-100) REVERT: C 130 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7670 (pm20) outliers start: 30 outliers final: 19 residues processed: 160 average time/residue: 1.2649 time to fit residues: 219.6754 Evaluate side-chains 157 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 134 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 470 HIS Chi-restraints excluded: chain A residue 613 CYS Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 661 SER Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 94 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 15 optimal weight: 0.0030 chunk 28 optimal weight: 0.1980 chunk 104 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 0.0870 chunk 91 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 overall best weight: 0.3768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.109616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.084459 restraints weight = 14165.482| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.11 r_work: 0.2840 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10761 Z= 0.140 Angle : 0.542 8.786 14571 Z= 0.266 Chirality : 0.039 0.193 1662 Planarity : 0.004 0.049 1828 Dihedral : 4.278 49.415 1529 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.52 % Allowed : 23.00 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 1.18 (0.24), residues: 1308 helix: 2.04 (0.20), residues: 680 sheet: -0.04 (0.38), residues: 188 loop : -0.84 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 536 HIS 0.004 0.001 HIS B 531 PHE 0.016 0.001 PHE B 493 TYR 0.013 0.001 TYR A 114 ARG 0.010 0.000 ARG D 44 =============================================================================== Job complete usr+sys time: 4332.57 seconds wall clock time: 77 minutes 24.84 seconds (4644.84 seconds total)