Starting phenix.real_space_refine on Wed Feb 14 21:27:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uc1_42112/02_2024/8uc1_42112.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uc1_42112/02_2024/8uc1_42112.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uc1_42112/02_2024/8uc1_42112.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uc1_42112/02_2024/8uc1_42112.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uc1_42112/02_2024/8uc1_42112.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uc1_42112/02_2024/8uc1_42112.pdb" } resolution = 3.4 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= 0.013 sd= 0.059 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: 5 Type Number sf(0) Gaussians S 50 5.16 5 Cl 2 4.86 5 C 6756 2.51 5 N 1660 2.21 5 O 1842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 30": "OE1" <-> "OE2" Residue "A GLU 40": "OE1" <-> "OE2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A ARG 150": "NH1" <-> "NH2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 40": "OE1" <-> "OE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B ARG 150": "NH1" <-> "NH2" Residue "B GLU 311": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10310 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5154 Classifications: {'peptide': 668} Link IDs: {'PTRANS': 31, 'TRANS': 636} Chain breaks: 1 Chain: "B" Number of atoms: 5154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5154 Classifications: {'peptide': 668} Link IDs: {'PTRANS': 31, 'TRANS': 636} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.02, per 1000 atoms: 0.58 Number of scatterers: 10310 At special positions: 0 Unit cell: (86.508, 114.276, 115.344, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 50 16.00 O 1842 8.00 N 1660 7.00 C 6756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.15 Conformation dependent library (CDL) restraints added in 1.9 seconds 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2464 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 3 sheets defined 70.2% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 41 through 51 removed outlier: 3.658A pdb=" N GLN A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'A' and resid 66 through 71 removed outlier: 3.553A pdb=" N TRP A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 74 No H-bonds generated for 'chain 'A' and resid 72 through 74' Processing helix chain 'A' and resid 78 through 105 removed outlier: 4.327A pdb=" N GLY A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Proline residue: A 96 - end of helix Processing helix chain 'A' and resid 109 through 116 removed outlier: 3.949A pdb=" N LEU A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 127 removed outlier: 3.757A pdb=" N MET A 122 " --> pdb=" O TYR A 118 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 152 Processing helix chain 'A' and resid 168 through 196 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 231 removed outlier: 4.326A pdb=" N LYS A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TYR A 228 " --> pdb=" O SER A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 253 Processing helix chain 'A' and resid 254 through 257 Processing helix chain 'A' and resid 258 through 282 Processing helix chain 'A' and resid 291 through 308 Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 335 through 366 removed outlier: 3.529A pdb=" N TYR A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL A 341 " --> pdb=" O HIS A 337 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 387 Processing helix chain 'A' and resid 397 through 407 removed outlier: 3.742A pdb=" N GLY A 407 " --> pdb=" O GLN A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 Processing helix chain 'A' and resid 430 through 435 removed outlier: 3.632A pdb=" N GLU A 433 " --> pdb=" O PHE A 430 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER A 434 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 448 removed outlier: 3.717A pdb=" N LEU A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 448 " --> pdb=" O VAL A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 456 through 465 removed outlier: 3.717A pdb=" N PHE A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 484 through 505 removed outlier: 3.915A pdb=" N LEU A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 490 " --> pdb=" O TYR A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 560 removed outlier: 3.532A pdb=" N THR A 560 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 577 Processing helix chain 'A' and resid 653 through 671 removed outlier: 3.710A pdb=" N VAL A 670 " --> pdb=" O GLU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 690 Processing helix chain 'A' and resid 695 through 700 Processing helix chain 'A' and resid 705 through 722 removed outlier: 3.734A pdb=" N GLN A 722 " --> pdb=" O ALA A 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 32 Processing helix chain 'B' and resid 41 through 51 removed outlier: 3.658A pdb=" N GLN B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 65 Processing helix chain 'B' and resid 66 through 71 removed outlier: 3.553A pdb=" N TRP B 70 " --> pdb=" O PRO B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 74 No H-bonds generated for 'chain 'B' and resid 72 through 74' Processing helix chain 'B' and resid 78 through 105 removed outlier: 4.327A pdb=" N GLY B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Proline residue: B 96 - end of helix Processing helix chain 'B' and resid 109 through 116 removed outlier: 3.949A pdb=" N LEU B 113 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 127 removed outlier: 3.757A pdb=" N MET B 122 " --> pdb=" O TYR B 118 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 125 " --> pdb=" O ILE B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 152 Processing helix chain 'B' and resid 168 through 196 Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 206 through 231 removed outlier: 4.326A pdb=" N LYS B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TYR B 228 " --> pdb=" O SER B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 253 Processing helix chain 'B' and resid 254 through 257 Processing helix chain 'B' and resid 258 through 282 Processing helix chain 'B' and resid 291 through 308 Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'B' and resid 335 through 366 removed outlier: 3.529A pdb=" N TYR B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL B 341 " --> pdb=" O HIS B 337 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 387 Processing helix chain 'B' and resid 397 through 407 removed outlier: 3.742A pdb=" N GLY B 407 " --> pdb=" O GLN B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 427 Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.632A pdb=" N GLU B 433 " --> pdb=" O PHE B 430 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER B 434 " --> pdb=" O LEU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 448 removed outlier: 3.717A pdb=" N LEU B 440 " --> pdb=" O PRO B 436 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 448 " --> pdb=" O VAL B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 456 through 465 removed outlier: 3.717A pdb=" N PHE B 460 " --> pdb=" O SER B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 482 Processing helix chain 'B' and resid 484 through 505 removed outlier: 3.915A pdb=" N LEU B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE B 489 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR B 490 " --> pdb=" O TYR B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 560 removed outlier: 3.532A pdb=" N THR B 560 " --> pdb=" O LEU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 577 Processing helix chain 'B' and resid 653 through 671 removed outlier: 3.710A pdb=" N VAL B 670 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 690 Processing helix chain 'B' and resid 695 through 700 Processing helix chain 'B' and resid 705 through 722 removed outlier: 3.734A pdb=" N GLN B 722 " --> pdb=" O ALA B 718 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 21 removed outlier: 3.595A pdb=" N VAL A 18 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 18 " --> pdb=" O VAL A 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522 removed outlier: 4.573A pdb=" N ILE A 537 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N GLN A 513 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 11.730A pdb=" N ILE A 535 " --> pdb=" O GLN A 513 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LYS A 536 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASP A 645 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N PHE A 538 " --> pdb=" O ASP A 645 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N PHE A 703 " --> pdb=" O VAL A 674 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU A 676 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 520 through 522 removed outlier: 4.573A pdb=" N ILE B 537 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N GLN B 513 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 11.730A pdb=" N ILE B 535 " --> pdb=" O GLN B 513 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LYS B 536 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASP B 645 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N PHE B 538 " --> pdb=" O ASP B 645 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N PHE B 703 " --> pdb=" O VAL B 674 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU B 676 " --> pdb=" O PHE B 703 " (cutoff:3.500A) 650 hydrogen bonds defined for protein. 1890 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: 3.21 Time building geometry restraints manager: 4.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1724 1.32 - 1.45: 2658 1.45 - 1.57: 6072 1.57 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 10536 Sorted by residual: bond pdb=" CE1 HIS B 337 " pdb=" NE2 HIS B 337 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.68e+01 bond pdb=" CE1 HIS A 337 " pdb=" NE2 HIS A 337 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.68e+01 bond pdb=" C PRO A 327 " pdb=" O PRO A 327 " ideal model delta sigma weight residual 1.243 1.209 0.034 8.50e-03 1.38e+04 1.58e+01 bond pdb=" C PRO B 327 " pdb=" O PRO B 327 " ideal model delta sigma weight residual 1.243 1.209 0.034 8.50e-03 1.38e+04 1.58e+01 bond pdb=" N GLU A 207 " pdb=" CA GLU A 207 " ideal model delta sigma weight residual 1.462 1.488 -0.026 8.50e-03 1.38e+04 9.12e+00 ... (remaining 10531 not shown) Histogram of bond angle deviations from ideal: 98.99 - 105.99: 260 105.99 - 113.00: 5783 113.00 - 120.00: 3706 120.00 - 127.00: 4487 127.00 - 134.01: 82 Bond angle restraints: 14318 Sorted by residual: angle pdb=" C LEU B 326 " pdb=" N PRO B 327 " pdb=" CA PRO B 327 " ideal model delta sigma weight residual 119.66 122.71 -3.05 7.20e-01 1.93e+00 1.79e+01 angle pdb=" C LEU A 326 " pdb=" N PRO A 327 " pdb=" CA PRO A 327 " ideal model delta sigma weight residual 119.66 122.71 -3.05 7.20e-01 1.93e+00 1.79e+01 angle pdb=" CB GLN B 504 " pdb=" CG GLN B 504 " pdb=" CD GLN B 504 " ideal model delta sigma weight residual 112.60 105.56 7.04 1.70e+00 3.46e-01 1.72e+01 angle pdb=" CB GLN A 504 " pdb=" CG GLN A 504 " pdb=" CD GLN A 504 " ideal model delta sigma weight residual 112.60 105.56 7.04 1.70e+00 3.46e-01 1.72e+01 angle pdb=" CA ASN B 382 " pdb=" C ASN B 382 " pdb=" O ASN B 382 " ideal model delta sigma weight residual 120.82 116.47 4.35 1.05e+00 9.07e-01 1.71e+01 ... (remaining 14313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 5538 17.18 - 34.37: 583 34.37 - 51.55: 85 51.55 - 68.73: 24 68.73 - 85.91: 6 Dihedral angle restraints: 6236 sinusoidal: 2388 harmonic: 3848 Sorted by residual: dihedral pdb=" CG ARG A 502 " pdb=" CD ARG A 502 " pdb=" NE ARG A 502 " pdb=" CZ ARG A 502 " ideal model delta sinusoidal sigma weight residual 180.00 138.56 41.44 2 1.50e+01 4.44e-03 9.34e+00 dihedral pdb=" CG ARG B 502 " pdb=" CD ARG B 502 " pdb=" NE ARG B 502 " pdb=" CZ ARG B 502 " ideal model delta sinusoidal sigma weight residual 180.00 138.56 41.44 2 1.50e+01 4.44e-03 9.34e+00 dihedral pdb=" CA ILE A 140 " pdb=" CB ILE A 140 " pdb=" CG1 ILE A 140 " pdb=" CD1 ILE A 140 " ideal model delta sinusoidal sigma weight residual 60.00 114.99 -54.99 3 1.50e+01 4.44e-03 9.32e+00 ... (remaining 6233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1165 0.043 - 0.087: 364 0.087 - 0.130: 127 0.130 - 0.173: 36 0.173 - 0.217: 14 Chirality restraints: 1706 Sorted by residual: chirality pdb=" CA ILE B 393 " pdb=" N ILE B 393 " pdb=" C ILE B 393 " pdb=" CB ILE B 393 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE A 393 " pdb=" N ILE A 393 " pdb=" C ILE A 393 " pdb=" CB ILE A 393 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA VAL B 532 " pdb=" N VAL B 532 " pdb=" C VAL B 532 " pdb=" CB VAL B 532 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.30e-01 ... (remaining 1703 not shown) Planarity restraints: 1784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 150 " -0.248 9.50e-02 1.11e+02 1.11e-01 7.60e+00 pdb=" NE ARG A 150 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 150 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 150 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 150 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 150 " 0.248 9.50e-02 1.11e+02 1.11e-01 7.60e+00 pdb=" NE ARG B 150 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG B 150 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 150 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 150 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 288 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO A 289 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 289 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 289 " 0.030 5.00e-02 4.00e+02 ... (remaining 1781 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1668 2.76 - 3.29: 10481 3.29 - 3.83: 17174 3.83 - 4.36: 19390 4.36 - 4.90: 34164 Nonbonded interactions: 82877 Sorted by model distance: nonbonded pdb=" O ALA A 495 " pdb=" OG1 THR A 498 " model vdw 2.220 2.440 nonbonded pdb=" O ALA B 495 " pdb=" OG1 THR B 498 " model vdw 2.220 2.440 nonbonded pdb=" OG1 THR B 128 " pdb=" OE1 GLU B 374 " model vdw 2.245 2.440 nonbonded pdb=" OG1 THR A 128 " pdb=" OE1 GLU A 374 " model vdw 2.245 2.440 nonbonded pdb=" O MET B 63 " pdb=" NE2 GLN B 373 " model vdw 2.320 2.520 ... (remaining 82872 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 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: 1.530 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: 4.080 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 31.210 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 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 : 0.005 0.041 10536 Z= 0.333 Angle : 0.723 7.845 14318 Z= 0.496 Chirality : 0.052 0.217 1706 Planarity : 0.006 0.111 1784 Dihedral : 14.103 85.914 3772 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.71 % Allowed : 10.93 % Favored : 88.36 % 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: 1.30 (0.24), residues: 1328 helix: 1.60 (0.18), residues: 824 sheet: 1.89 (0.76), residues: 52 loop : -0.60 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 70 HIS 0.001 0.000 HIS B 220 PHE 0.012 0.001 PHE B 213 TYR 0.028 0.001 TYR B 123 ARG 0.002 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 114 time to evaluate : 1.177 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 120 average time/residue: 0.2200 time to fit residues: 38.2423 Evaluate side-chains 109 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain B residue 342 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 103 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 119 optimal weight: 0.4980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 HIS ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN A 707 HIS B 25 HIS B 220 HIS ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN B 707 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10536 Z= 0.250 Angle : 0.546 7.511 14318 Z= 0.281 Chirality : 0.043 0.146 1706 Planarity : 0.004 0.048 1784 Dihedral : 3.920 18.943 1430 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.00 % Allowed : 11.38 % Favored : 85.63 % 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: 1.59 (0.24), residues: 1328 helix: 1.73 (0.18), residues: 862 sheet: 3.15 (0.77), residues: 36 loop : -0.48 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 472 HIS 0.002 0.001 HIS A 337 PHE 0.014 0.001 PHE A 294 TYR 0.015 0.001 TYR B 16 ARG 0.001 0.000 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 114 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 10 residues processed: 136 average time/residue: 0.2213 time to fit residues: 43.3069 Evaluate side-chains 120 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 260 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 119 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10536 Z= 0.239 Angle : 0.522 5.659 14318 Z= 0.270 Chirality : 0.043 0.157 1706 Planarity : 0.004 0.042 1784 Dihedral : 3.896 14.829 1426 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.07 % Favored : 95.78 % Rotamer: Outliers : 1.94 % Allowed : 13.84 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.24), residues: 1328 helix: 1.71 (0.18), residues: 864 sheet: 3.02 (0.78), residues: 36 loop : -0.40 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 70 HIS 0.002 0.001 HIS A 337 PHE 0.016 0.001 PHE A 111 TYR 0.013 0.001 TYR B 16 ARG 0.001 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 114 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 130 average time/residue: 0.2099 time to fit residues: 40.0983 Evaluate side-chains 125 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 333 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 62 optimal weight: 0.0270 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10536 Z= 0.176 Angle : 0.479 6.091 14318 Z= 0.246 Chirality : 0.041 0.125 1706 Planarity : 0.004 0.037 1784 Dihedral : 3.824 15.349 1426 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.54 % Favored : 96.31 % Rotamer: Outliers : 2.91 % Allowed : 13.40 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.24), residues: 1328 helix: 1.76 (0.18), residues: 870 sheet: 1.97 (0.73), residues: 52 loop : -0.15 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 70 HIS 0.001 0.000 HIS B 707 PHE 0.025 0.001 PHE A 111 TYR 0.010 0.001 TYR A 16 ARG 0.001 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 108 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 21 residues processed: 133 average time/residue: 0.2111 time to fit residues: 40.9236 Evaluate side-chains 122 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 101 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 342 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 GLN ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10536 Z= 0.320 Angle : 0.556 11.866 14318 Z= 0.283 Chirality : 0.043 0.135 1706 Planarity : 0.004 0.034 1784 Dihedral : 3.923 15.772 1426 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.77 % Favored : 96.08 % Rotamer: Outliers : 3.00 % Allowed : 14.46 % Favored : 82.54 % 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: 1.60 (0.24), residues: 1328 helix: 1.65 (0.18), residues: 872 sheet: 1.82 (0.72), residues: 52 loop : -0.25 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 70 HIS 0.003 0.001 HIS B 640 PHE 0.023 0.002 PHE A 111 TYR 0.013 0.002 TYR A 545 ARG 0.001 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 108 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 26 residues processed: 132 average time/residue: 0.2066 time to fit residues: 39.9449 Evaluate side-chains 130 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 104 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 545 TYR Chi-restraints excluded: chain B residue 698 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10536 Z= 0.227 Angle : 0.510 10.108 14318 Z= 0.259 Chirality : 0.042 0.127 1706 Planarity : 0.004 0.034 1784 Dihedral : 3.896 16.867 1426 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.94 % Favored : 96.91 % Rotamer: Outliers : 3.26 % Allowed : 14.02 % Favored : 82.72 % 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: 1.63 (0.24), residues: 1328 helix: 1.67 (0.18), residues: 872 sheet: 1.73 (0.73), residues: 52 loop : -0.23 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 472 HIS 0.002 0.001 HIS A 707 PHE 0.021 0.001 PHE A 111 TYR 0.010 0.001 TYR B 16 ARG 0.001 0.000 ARG A 716 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 101 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 27 residues processed: 130 average time/residue: 0.2279 time to fit residues: 42.4639 Evaluate side-chains 126 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 545 TYR Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 395 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10536 Z= 0.317 Angle : 0.558 9.073 14318 Z= 0.284 Chirality : 0.043 0.136 1706 Planarity : 0.004 0.033 1784 Dihedral : 3.955 17.685 1426 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.54 % Favored : 96.31 % Rotamer: Outliers : 3.26 % Allowed : 14.29 % Favored : 82.45 % 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: 1.51 (0.24), residues: 1328 helix: 1.58 (0.18), residues: 872 sheet: 1.72 (0.72), residues: 52 loop : -0.27 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 472 HIS 0.003 0.001 HIS B 707 PHE 0.022 0.001 PHE A 111 TYR 0.012 0.002 TYR B 545 ARG 0.001 0.000 ARG B 716 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 101 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 33 residues processed: 130 average time/residue: 0.2226 time to fit residues: 42.0110 Evaluate side-chains 133 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 100 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 545 TYR Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 545 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10536 Z= 0.185 Angle : 0.509 8.532 14318 Z= 0.256 Chirality : 0.041 0.128 1706 Planarity : 0.003 0.034 1784 Dihedral : 3.877 17.957 1426 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.16 % Favored : 96.69 % Rotamer: Outliers : 3.00 % Allowed : 14.90 % Favored : 82.10 % 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: 1.71 (0.24), residues: 1328 helix: 1.73 (0.18), residues: 872 sheet: 1.69 (0.73), residues: 52 loop : -0.18 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 70 HIS 0.003 0.001 HIS B 131 PHE 0.018 0.001 PHE B 111 TYR 0.014 0.001 TYR B 123 ARG 0.002 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 101 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 TYR cc_start: 0.8606 (m-80) cc_final: 0.8294 (m-80) REVERT: B 228 TYR cc_start: 0.8612 (m-80) cc_final: 0.8294 (m-80) outliers start: 34 outliers final: 30 residues processed: 127 average time/residue: 0.2119 time to fit residues: 39.6357 Evaluate side-chains 129 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 99 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 698 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 0.2980 chunk 36 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 112 optimal weight: 0.5980 chunk 77 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10536 Z= 0.183 Angle : 0.502 8.093 14318 Z= 0.253 Chirality : 0.041 0.164 1706 Planarity : 0.003 0.034 1784 Dihedral : 3.822 17.628 1426 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.54 % Favored : 96.31 % Rotamer: Outliers : 3.17 % Allowed : 14.64 % Favored : 82.19 % 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: 1.80 (0.24), residues: 1328 helix: 1.79 (0.18), residues: 872 sheet: 1.72 (0.72), residues: 52 loop : -0.10 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 70 HIS 0.002 0.001 HIS B 640 PHE 0.017 0.001 PHE A 111 TYR 0.011 0.001 TYR A 123 ARG 0.002 0.000 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 101 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 32 residues processed: 131 average time/residue: 0.2258 time to fit residues: 42.1113 Evaluate side-chains 130 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 98 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 CYS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain B residue 52 CYS Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 395 CYS Chi-restraints excluded: chain B residue 698 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 121 optimal weight: 0.0870 chunk 104 optimal weight: 0.5980 chunk 10 optimal weight: 0.0670 chunk 80 optimal weight: 0.0170 chunk 64 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10536 Z= 0.142 Angle : 0.493 7.746 14318 Z= 0.247 Chirality : 0.041 0.158 1706 Planarity : 0.003 0.035 1784 Dihedral : 3.783 19.044 1426 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.16 % Favored : 96.69 % Rotamer: Outliers : 2.29 % Allowed : 15.96 % Favored : 81.75 % 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: 1.98 (0.24), residues: 1328 helix: 1.88 (0.18), residues: 872 sheet: 1.74 (0.75), residues: 50 loop : 0.08 (0.33), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 70 HIS 0.001 0.000 HIS B 704 PHE 0.014 0.001 PHE A 111 TYR 0.020 0.001 TYR B 123 ARG 0.002 0.000 ARG B 150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 98 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 25 residues processed: 118 average time/residue: 0.2268 time to fit residues: 38.8379 Evaluate side-chains 122 residues out of total 1134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 260 CYS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 260 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 395 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 104 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 107 optimal weight: 0.0770 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 GLN ** 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 = 0.4032 r_free = 0.4032 target = 0.177139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.129075 restraints weight = 11608.456| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 3.03 r_work: 0.3142 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10536 Z= 0.172 Angle : 0.501 7.676 14318 Z= 0.251 Chirality : 0.041 0.158 1706 Planarity : 0.003 0.035 1784 Dihedral : 3.779 20.698 1426 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.54 % Favored : 96.31 % Rotamer: Outliers : 2.29 % Allowed : 16.05 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.24), residues: 1328 helix: 1.89 (0.18), residues: 872 sheet: 1.73 (0.75), residues: 50 loop : 0.05 (0.33), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 70 HIS 0.002 0.000 HIS B 707 PHE 0.015 0.001 PHE A 111 TYR 0.018 0.001 TYR A 123 ARG 0.002 0.000 ARG A 150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2025.02 seconds wall clock time: 37 minutes 44.18 seconds (2264.18 seconds total)