Starting phenix.real_space_refine on Wed Feb 14 08:58:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ffc_4256/02_2024/6ffc_4256_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ffc_4256/02_2024/6ffc_4256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ffc_4256/02_2024/6ffc_4256.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ffc_4256/02_2024/6ffc_4256.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ffc_4256/02_2024/6ffc_4256_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ffc_4256/02_2024/6ffc_4256_updated.pdb" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 58 5.16 5 C 5836 2.51 5 N 1472 2.21 5 O 1608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 96": "NH1" <-> "NH2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8974 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4449 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 19, 'TRANS': 552} Chain breaks: 3 Chain: "B" Number of atoms: 4449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4449 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 19, 'TRANS': 552} Chain breaks: 3 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'BWQ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'BWQ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.03, per 1000 atoms: 0.56 Number of scatterers: 8974 At special positions: 0 Unit cell: (96.628, 84.448, 126.672, 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 58 16.00 O 1608 8.00 N 1472 7.00 C 5836 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.04 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.04 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.04 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: 3.18 Conformation dependent library (CDL) restraints added in 1.7 seconds 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 6 sheets defined 55.0% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 86 through 93 Processing helix chain 'A' and resid 117 through 120 No H-bonds generated for 'chain 'A' and resid 117 through 120' Processing helix chain 'A' and resid 136 through 147 Processing helix chain 'A' and resid 154 through 168 Processing helix chain 'A' and resid 188 through 199 removed outlier: 3.927A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 234 removed outlier: 4.097A pdb=" N GLN A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 removed outlier: 4.572A pdb=" N LEU A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.415A pdb=" N GLY A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 299 Processing helix chain 'A' and resid 329 through 337 removed outlier: 3.788A pdb=" N GLU A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 353 removed outlier: 3.571A pdb=" N GLU A 344 " --> pdb=" O SER A 340 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 345 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 390 Processing helix chain 'A' and resid 393 through 412 removed outlier: 4.519A pdb=" N GLN A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 442 removed outlier: 3.926A pdb=" N VAL A 442 " --> pdb=" O CYS A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 450 No H-bonds generated for 'chain 'A' and resid 447 through 450' Processing helix chain 'A' and resid 452 through 460 Processing helix chain 'A' and resid 466 through 477 Processing helix chain 'A' and resid 480 through 497 Proline residue: A 485 - end of helix removed outlier: 4.722A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 497 " --> pdb=" O VAL A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 528 Processing helix chain 'A' and resid 535 through 548 Processing helix chain 'A' and resid 566 through 570 removed outlier: 3.660A pdb=" N GLN A 569 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR A 570 " --> pdb=" O TRP A 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 566 through 570' Processing helix chain 'A' and resid 573 through 585 Processing helix chain 'A' and resid 601 through 604 removed outlier: 3.785A pdb=" N ASN A 604 " --> pdb=" O ASN A 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 601 through 604' Processing helix chain 'A' and resid 610 through 616 removed outlier: 3.653A pdb=" N LYS A 616 " --> pdb=" O GLU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 649 removed outlier: 4.974A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 93 Processing helix chain 'B' and resid 117 through 120 No H-bonds generated for 'chain 'B' and resid 117 through 120' Processing helix chain 'B' and resid 136 through 147 Processing helix chain 'B' and resid 154 through 168 Processing helix chain 'B' and resid 188 through 199 removed outlier: 3.928A pdb=" N GLU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 234 removed outlier: 4.097A pdb=" N GLN B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 removed outlier: 4.571A pdb=" N LEU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 280 removed outlier: 4.414A pdb=" N GLY B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 299 Processing helix chain 'B' and resid 329 through 337 removed outlier: 3.788A pdb=" N GLU B 334 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 353 removed outlier: 3.571A pdb=" N GLU B 344 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 345 " --> pdb=" O PHE B 341 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 390 Processing helix chain 'B' and resid 393 through 412 removed outlier: 4.520A pdb=" N GLN B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 442 removed outlier: 3.926A pdb=" N VAL B 442 " --> pdb=" O CYS B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 450 No H-bonds generated for 'chain 'B' and resid 447 through 450' Processing helix chain 'B' and resid 452 through 460 Processing helix chain 'B' and resid 466 through 477 Processing helix chain 'B' and resid 479 through 497 Proline residue: B 485 - end of helix removed outlier: 4.721A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 497 " --> pdb=" O VAL B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 528 Processing helix chain 'B' and resid 535 through 548 Processing helix chain 'B' and resid 566 through 570 removed outlier: 3.659A pdb=" N GLN B 569 " --> pdb=" O SER B 566 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR B 570 " --> pdb=" O TRP B 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 566 through 570' Processing helix chain 'B' and resid 573 through 585 Processing helix chain 'B' and resid 601 through 604 removed outlier: 3.786A pdb=" N ASN B 604 " --> pdb=" O ASN B 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 601 through 604' Processing helix chain 'B' and resid 610 through 616 removed outlier: 3.652A pdb=" N LYS B 616 " --> pdb=" O GLU B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 649 removed outlier: 4.974A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 69 through 71 removed outlier: 3.686A pdb=" N ASP A 105 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 263 through 269 removed outlier: 6.428A pdb=" N LEU A 258 " --> pdb=" O MET A 265 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N HIS A 267 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU A 256 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE A 238 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ILE A 78 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N PHE A 240 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N GLY A 80 " --> pdb=" O PHE A 240 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 44 through 47 removed outlier: 6.531A pdb=" N VAL A 46 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLU A 62 " --> pdb=" O VAL A 46 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 69 through 71 removed outlier: 3.686A pdb=" N ASP B 105 " --> pdb=" O HIS B 40 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 263 through 269 removed outlier: 6.427A pdb=" N LEU B 258 " --> pdb=" O MET B 265 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N HIS B 267 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU B 256 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE B 238 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ILE B 78 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N PHE B 240 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N GLY B 80 " --> pdb=" O PHE B 240 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 44 through 47 removed outlier: 6.530A pdb=" N VAL B 46 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLU B 62 " --> pdb=" O VAL B 46 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1245 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: 2.60 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1406 1.31 - 1.45: 2506 1.45 - 1.58: 5162 1.58 - 1.71: 0 1.71 - 1.84: 94 Bond restraints: 9168 Sorted by residual: bond pdb=" C36 BWQ B 701 " pdb=" O37 BWQ B 701 " ideal model delta sigma weight residual 1.220 1.393 -0.173 2.00e-02 2.50e+03 7.44e+01 bond pdb=" C36 BWQ A 701 " pdb=" O37 BWQ A 701 " ideal model delta sigma weight residual 1.220 1.393 -0.173 2.00e-02 2.50e+03 7.44e+01 bond pdb=" C23 BWQ B 701 " pdb=" O24 BWQ B 701 " ideal model delta sigma weight residual 1.222 1.390 -0.168 2.00e-02 2.50e+03 7.04e+01 bond pdb=" C23 BWQ A 701 " pdb=" O24 BWQ A 701 " ideal model delta sigma weight residual 1.222 1.389 -0.167 2.00e-02 2.50e+03 7.00e+01 bond pdb=" C19 BWQ A 701 " pdb=" C20 BWQ A 701 " ideal model delta sigma weight residual 1.431 1.566 -0.135 2.00e-02 2.50e+03 4.54e+01 ... (remaining 9163 not shown) Histogram of bond angle deviations from ideal: 97.42 - 105.87: 185 105.87 - 114.31: 5420 114.31 - 122.76: 6196 122.76 - 131.20: 582 131.20 - 139.65: 33 Bond angle restraints: 12416 Sorted by residual: angle pdb=" C SER B 572 " pdb=" N ILE B 573 " pdb=" CA ILE B 573 " ideal model delta sigma weight residual 120.24 126.49 -6.25 6.30e-01 2.52e+00 9.84e+01 angle pdb=" C SER A 572 " pdb=" N ILE A 573 " pdb=" CA ILE A 573 " ideal model delta sigma weight residual 120.24 126.47 -6.23 6.30e-01 2.52e+00 9.77e+01 angle pdb=" C VAL A 445 " pdb=" N GLU A 446 " pdb=" CA GLU A 446 " ideal model delta sigma weight residual 120.38 127.88 -7.50 1.46e+00 4.69e-01 2.64e+01 angle pdb=" C VAL B 445 " pdb=" N GLU B 446 " pdb=" CA GLU B 446 " ideal model delta sigma weight residual 120.38 127.81 -7.43 1.46e+00 4.69e-01 2.59e+01 angle pdb=" C06 BWQ A 701 " pdb=" N07 BWQ A 701 " pdb=" C08 BWQ A 701 " ideal model delta sigma weight residual 109.00 123.45 -14.45 3.00e+00 1.11e-01 2.32e+01 ... (remaining 12411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.16: 5389 27.16 - 54.33: 72 54.33 - 81.49: 6 81.49 - 108.65: 2 108.65 - 135.82: 6 Dihedral angle restraints: 5475 sinusoidal: 2183 harmonic: 3292 Sorted by residual: dihedral pdb=" CA ASN A 601 " pdb=" C ASN A 601 " pdb=" N PRO A 602 " pdb=" CA PRO A 602 " ideal model delta harmonic sigma weight residual -180.00 -130.70 -49.30 0 5.00e+00 4.00e-02 9.72e+01 dihedral pdb=" CA ASN B 601 " pdb=" C ASN B 601 " pdb=" N PRO B 602 " pdb=" CA PRO B 602 " ideal model delta harmonic sigma weight residual -180.00 -130.74 -49.26 0 5.00e+00 4.00e-02 9.71e+01 dihedral pdb=" CA PRO B 602 " pdb=" C PRO B 602 " pdb=" N CYS B 603 " pdb=" CA CYS B 603 " ideal model delta harmonic sigma weight residual 180.00 155.55 24.45 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 5472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1238 0.075 - 0.150: 164 0.150 - 0.226: 22 0.226 - 0.301: 6 0.301 - 0.376: 2 Chirality restraints: 1432 Sorted by residual: chirality pdb=" CB VAL B 173 " pdb=" CA VAL B 173 " pdb=" CG1 VAL B 173 " pdb=" CG2 VAL B 173 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CB VAL A 173 " pdb=" CA VAL A 173 " pdb=" CG1 VAL A 173 " pdb=" CG2 VAL A 173 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" C22 BWQ A 701 " pdb=" C21 BWQ A 701 " pdb=" C23 BWQ A 701 " pdb=" N38 BWQ A 701 " both_signs ideal model delta sigma weight residual False -2.33 -2.59 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 1429 not shown) Planarity restraints: 1540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C05 BWQ B 701 " -0.184 2.00e-02 2.50e+03 2.20e-01 7.24e+02 pdb=" C22 BWQ B 701 " 0.309 2.00e-02 2.50e+03 pdb=" C26 BWQ B 701 " -0.200 2.00e-02 2.50e+03 pdb=" C36 BWQ B 701 " -0.026 2.00e-02 2.50e+03 pdb=" N38 BWQ B 701 " -0.189 2.00e-02 2.50e+03 pdb=" O37 BWQ B 701 " 0.290 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 BWQ B 701 " 0.032 2.00e-02 2.50e+03 2.14e-01 5.74e+02 pdb=" C23 BWQ B 701 " 0.063 2.00e-02 2.50e+03 pdb=" C26 BWQ B 701 " -0.264 2.00e-02 2.50e+03 pdb=" N25 BWQ B 701 " 0.349 2.00e-02 2.50e+03 pdb=" O24 BWQ B 701 " -0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 BWQ A 701 " -0.046 2.00e-02 2.50e+03 8.93e-02 1.20e+02 pdb=" C22 BWQ A 701 " -0.097 2.00e-02 2.50e+03 pdb=" C26 BWQ A 701 " -0.010 2.00e-02 2.50e+03 pdb=" C36 BWQ A 701 " 0.038 2.00e-02 2.50e+03 pdb=" N38 BWQ A 701 " 0.176 2.00e-02 2.50e+03 pdb=" O37 BWQ A 701 " -0.060 2.00e-02 2.50e+03 ... (remaining 1537 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1823 2.77 - 3.30: 8354 3.30 - 3.83: 14630 3.83 - 4.37: 17131 4.37 - 4.90: 30407 Nonbonded interactions: 72345 Sorted by model distance: nonbonded pdb=" OH TYR A 494 " pdb=" O LYS A 500 " model vdw 2.235 2.440 nonbonded pdb=" OH TYR B 494 " pdb=" O LYS B 500 " model vdw 2.236 2.440 nonbonded pdb=" NH1 ARG B 426 " pdb=" OE2 GLU B 585 " model vdw 2.341 2.520 nonbonded pdb=" NH1 ARG A 426 " pdb=" OE2 GLU A 585 " model vdw 2.341 2.520 nonbonded pdb=" OG SER A 218 " pdb=" ND2 ASN B 299 " model vdw 2.360 2.520 ... (remaining 72340 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' 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 group one per residue 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 6.950 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 26.560 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 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 : 0.009 0.173 9168 Z= 0.609 Angle : 1.091 14.446 12416 Z= 0.585 Chirality : 0.057 0.376 1432 Planarity : 0.010 0.220 1540 Dihedral : 11.436 135.815 3354 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.90 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -3.27 (0.20), residues: 1128 helix: -1.94 (0.16), residues: 658 sheet: -0.72 (0.66), residues: 48 loop : -2.52 (0.25), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 624 HIS 0.015 0.002 HIS A 583 PHE 0.031 0.004 PHE A 489 TYR 0.021 0.002 TYR B 342 ARG 0.012 0.001 ARG B 383 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 348 GLU cc_start: 0.7797 (tp30) cc_final: 0.7404 (tm-30) REVERT: A 385 PHE cc_start: 0.8823 (t80) cc_final: 0.8528 (t80) REVERT: B 331 LYS cc_start: 0.8247 (tttm) cc_final: 0.7986 (mptt) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.2321 time to fit residues: 68.7794 Evaluate side-chains 112 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 46 optimal weight: 0.5980 chunk 89 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 116 ASN A 166 GLN A 425 ASN A 437 GLN ** A 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN B 299 ASN B 425 ASN B 437 GLN B 582 GLN ** B 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9168 Z= 0.182 Angle : 0.609 8.578 12416 Z= 0.302 Chirality : 0.041 0.154 1432 Planarity : 0.004 0.052 1540 Dihedral : 11.544 140.813 1310 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.46 % Allowed : 9.24 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -1.23 (0.24), residues: 1128 helix: -0.15 (0.19), residues: 660 sheet: -0.23 (0.56), residues: 66 loop : -1.94 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 627 HIS 0.005 0.001 HIS A 583 PHE 0.021 0.002 PHE B 293 TYR 0.012 0.001 TYR A 463 ARG 0.003 0.000 ARG B 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 139 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 ASP cc_start: 0.8063 (t70) cc_final: 0.7705 (t0) REVERT: A 475 LEU cc_start: 0.8682 (tp) cc_final: 0.8429 (mp) REVERT: B 292 ASP cc_start: 0.9061 (m-30) cc_final: 0.8743 (m-30) REVERT: B 331 LYS cc_start: 0.8299 (tttm) cc_final: 0.7992 (mptt) REVERT: B 585 GLU cc_start: 0.7685 (tp30) cc_final: 0.7475 (tp30) outliers start: 24 outliers final: 15 residues processed: 154 average time/residue: 0.1864 time to fit residues: 40.9637 Evaluate side-chains 130 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 486 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 0.0070 chunk 28 optimal weight: 9.9990 chunk 103 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** A 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 GLN ** B 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9168 Z= 0.178 Angle : 0.562 7.595 12416 Z= 0.275 Chirality : 0.040 0.191 1432 Planarity : 0.003 0.030 1540 Dihedral : 11.053 140.526 1310 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.77 % Allowed : 10.57 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.25), residues: 1128 helix: 0.87 (0.21), residues: 652 sheet: 0.00 (0.58), residues: 66 loop : -1.59 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.005 0.001 HIS A 583 PHE 0.012 0.001 PHE A 39 TYR 0.014 0.001 TYR A 463 ARG 0.002 0.000 ARG B 246 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 128 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 296 ASP cc_start: 0.7983 (t70) cc_final: 0.7675 (t0) REVERT: A 330 GLU cc_start: 0.6920 (pm20) cc_final: 0.6687 (pm20) REVERT: A 475 LEU cc_start: 0.8753 (tp) cc_final: 0.8381 (mp) REVERT: B 292 ASP cc_start: 0.9082 (m-30) cc_final: 0.8723 (m-30) REVERT: B 331 LYS cc_start: 0.8323 (tttm) cc_final: 0.8026 (mptt) outliers start: 27 outliers final: 16 residues processed: 143 average time/residue: 0.1848 time to fit residues: 38.3989 Evaluate side-chains 124 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 486 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9168 Z= 0.293 Angle : 0.612 9.349 12416 Z= 0.300 Chirality : 0.043 0.188 1432 Planarity : 0.003 0.025 1540 Dihedral : 10.997 140.989 1310 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.29 % Allowed : 12.01 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: 0.24 (0.26), residues: 1128 helix: 1.15 (0.21), residues: 650 sheet: 0.01 (0.61), residues: 66 loop : -1.42 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 379 HIS 0.005 0.001 HIS B 583 PHE 0.024 0.002 PHE B 266 TYR 0.010 0.001 TYR A 342 ARG 0.002 0.000 ARG B 246 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 121 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: A 47 LYS cc_start: 0.8615 (mtmm) cc_final: 0.8413 (mttp) REVERT: A 296 ASP cc_start: 0.7983 (t70) cc_final: 0.7658 (t0) REVERT: A 330 GLU cc_start: 0.6966 (pm20) cc_final: 0.6760 (pm20) REVERT: A 585 GLU cc_start: 0.7716 (tp30) cc_final: 0.7462 (tp30) REVERT: B 71 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7034 (mmt) REVERT: B 292 ASP cc_start: 0.9076 (m-30) cc_final: 0.8742 (m-30) REVERT: B 331 LYS cc_start: 0.8465 (tttm) cc_final: 0.8131 (mptt) outliers start: 32 outliers final: 22 residues processed: 140 average time/residue: 0.1780 time to fit residues: 36.2140 Evaluate side-chains 134 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 489 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 ASN A 166 GLN A 583 HIS ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 9168 Z= 0.411 Angle : 0.679 11.382 12416 Z= 0.332 Chirality : 0.045 0.154 1432 Planarity : 0.003 0.023 1540 Dihedral : 10.880 146.024 1310 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.41 % Allowed : 12.32 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: 0.20 (0.26), residues: 1128 helix: 1.05 (0.21), residues: 650 sheet: 0.24 (0.65), residues: 62 loop : -1.32 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 379 HIS 0.005 0.001 HIS B 40 PHE 0.031 0.002 PHE A 293 TYR 0.013 0.002 TYR B 463 ARG 0.002 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 121 time to evaluate : 0.891 Fit side-chains REVERT: A 296 ASP cc_start: 0.7937 (t70) cc_final: 0.7651 (t0) REVERT: B 71 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.6820 (mmt) REVERT: B 292 ASP cc_start: 0.9083 (m-30) cc_final: 0.8811 (m-30) REVERT: B 331 LYS cc_start: 0.8417 (tttm) cc_final: 0.8112 (mptt) outliers start: 43 outliers final: 29 residues processed: 148 average time/residue: 0.1852 time to fit residues: 40.0649 Evaluate side-chains 139 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 109 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 489 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.1980 chunk 99 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 0.0970 chunk 27 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 51 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9168 Z= 0.172 Angle : 0.568 10.074 12416 Z= 0.275 Chirality : 0.041 0.200 1432 Planarity : 0.003 0.023 1540 Dihedral : 10.603 149.647 1310 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.16 % Allowed : 15.30 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 0.71 (0.26), residues: 1128 helix: 1.46 (0.21), residues: 652 sheet: 0.39 (0.64), residues: 62 loop : -1.13 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.004 0.001 HIS B 40 PHE 0.022 0.001 PHE A 293 TYR 0.011 0.001 TYR B 463 ARG 0.003 0.000 ARG B 246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 1.026 Fit side-chains REVERT: A 296 ASP cc_start: 0.7817 (t70) cc_final: 0.7614 (t0) REVERT: A 483 MET cc_start: 0.7351 (mtt) cc_final: 0.7064 (mtm) REVERT: B 292 ASP cc_start: 0.9070 (m-30) cc_final: 0.8760 (m-30) REVERT: B 331 LYS cc_start: 0.8351 (tttm) cc_final: 0.8054 (mptt) outliers start: 21 outliers final: 12 residues processed: 138 average time/residue: 0.1823 time to fit residues: 36.8627 Evaluate side-chains 126 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 489 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9168 Z= 0.213 Angle : 0.576 9.952 12416 Z= 0.278 Chirality : 0.041 0.159 1432 Planarity : 0.003 0.022 1540 Dihedral : 10.335 149.179 1310 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.85 % Allowed : 16.53 % Favored : 81.62 % 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: 0.88 (0.26), residues: 1128 helix: 1.62 (0.21), residues: 652 sheet: 0.62 (0.64), residues: 62 loop : -1.11 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 379 HIS 0.004 0.001 HIS A 40 PHE 0.013 0.001 PHE B 578 TYR 0.007 0.001 TYR A 342 ARG 0.002 0.000 ARG B 246 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 1.078 Fit side-chains REVERT: A 483 MET cc_start: 0.7377 (mtt) cc_final: 0.7113 (mtm) REVERT: B 292 ASP cc_start: 0.9071 (m-30) cc_final: 0.8788 (m-30) REVERT: B 331 LYS cc_start: 0.8324 (tttm) cc_final: 0.8034 (mptt) REVERT: B 585 GLU cc_start: 0.8072 (tp30) cc_final: 0.7793 (tp30) outliers start: 18 outliers final: 14 residues processed: 131 average time/residue: 0.1703 time to fit residues: 32.9768 Evaluate side-chains 125 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 489 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 105 optimal weight: 0.0980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9168 Z= 0.233 Angle : 0.598 9.976 12416 Z= 0.286 Chirality : 0.041 0.152 1432 Planarity : 0.003 0.022 1540 Dihedral : 10.275 148.117 1310 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.05 % Allowed : 16.43 % Favored : 81.52 % 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: 1.07 (0.26), residues: 1128 helix: 1.94 (0.21), residues: 628 sheet: 0.46 (0.59), residues: 72 loop : -1.16 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 379 HIS 0.003 0.001 HIS A 350 PHE 0.013 0.001 PHE B 578 TYR 0.014 0.001 TYR B 463 ARG 0.001 0.000 ARG B 246 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 1.042 Fit side-chains REVERT: A 483 MET cc_start: 0.7379 (mtt) cc_final: 0.7104 (mtm) REVERT: B 292 ASP cc_start: 0.9057 (m-30) cc_final: 0.8802 (m-30) REVERT: B 331 LYS cc_start: 0.8333 (tttm) cc_final: 0.8061 (mptt) REVERT: B 463 TYR cc_start: 0.9308 (m-10) cc_final: 0.9088 (m-80) outliers start: 20 outliers final: 16 residues processed: 127 average time/residue: 0.1771 time to fit residues: 33.1912 Evaluate side-chains 130 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 493 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 108 optimal weight: 0.0970 chunk 66 optimal weight: 4.9990 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 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9168 Z= 0.207 Angle : 0.585 9.899 12416 Z= 0.280 Chirality : 0.041 0.145 1432 Planarity : 0.003 0.022 1540 Dihedral : 10.253 147.436 1310 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.75 % Allowed : 16.84 % Favored : 81.42 % 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: 1.17 (0.26), residues: 1128 helix: 2.03 (0.21), residues: 628 sheet: 0.52 (0.60), residues: 72 loop : -1.13 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 379 HIS 0.002 0.001 HIS A 267 PHE 0.012 0.001 PHE B 578 TYR 0.014 0.001 TYR B 463 ARG 0.002 0.000 ARG B 246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 0.923 Fit side-chains REVERT: A 483 MET cc_start: 0.7356 (mtt) cc_final: 0.7121 (mtm) REVERT: B 331 LYS cc_start: 0.8298 (tttm) cc_final: 0.8018 (mptt) outliers start: 17 outliers final: 17 residues processed: 129 average time/residue: 0.1746 time to fit residues: 33.3690 Evaluate side-chains 131 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 489 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 104 optimal weight: 0.0870 chunk 90 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9168 Z= 0.195 Angle : 0.575 9.204 12416 Z= 0.276 Chirality : 0.040 0.143 1432 Planarity : 0.003 0.022 1540 Dihedral : 10.210 146.253 1310 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.75 % Allowed : 16.84 % Favored : 81.42 % 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: 1.23 (0.26), residues: 1128 helix: 2.08 (0.21), residues: 628 sheet: 0.62 (0.59), residues: 72 loop : -1.13 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 379 HIS 0.002 0.001 HIS A 267 PHE 0.026 0.001 PHE A 293 TYR 0.013 0.001 TYR B 463 ARG 0.002 0.000 ARG B 246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 0.903 Fit side-chains REVERT: A 475 LEU cc_start: 0.8715 (tp) cc_final: 0.8409 (mp) REVERT: A 483 MET cc_start: 0.7360 (mtt) cc_final: 0.7122 (mtm) REVERT: B 331 LYS cc_start: 0.8272 (tttm) cc_final: 0.8013 (mptt) outliers start: 17 outliers final: 15 residues processed: 131 average time/residue: 0.1793 time to fit residues: 34.4430 Evaluate side-chains 129 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 493 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 90 optimal weight: 0.0170 chunk 37 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.150400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.119127 restraints weight = 11012.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.122272 restraints weight = 6576.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.124416 restraints weight = 4767.859| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9168 Z= 0.197 Angle : 0.577 11.103 12416 Z= 0.277 Chirality : 0.040 0.145 1432 Planarity : 0.003 0.023 1540 Dihedral : 10.171 145.503 1310 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.05 % Allowed : 16.84 % Favored : 81.11 % 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: 1.23 (0.26), residues: 1128 helix: 2.07 (0.21), residues: 628 sheet: 0.66 (0.59), residues: 72 loop : -1.12 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 379 HIS 0.002 0.001 HIS B 267 PHE 0.026 0.001 PHE A 293 TYR 0.012 0.001 TYR B 463 ARG 0.002 0.000 ARG B 246 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1845.41 seconds wall clock time: 35 minutes 13.02 seconds (2113.02 seconds total)