Starting phenix.real_space_refine on Wed May 14 00:25:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8puw_17949/05_2025/8puw_17949.cif Found real_map, /net/cci-nas-00/data/ceres_data/8puw_17949/05_2025/8puw_17949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8puw_17949/05_2025/8puw_17949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8puw_17949/05_2025/8puw_17949.map" model { file = "/net/cci-nas-00/data/ceres_data/8puw_17949/05_2025/8puw_17949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8puw_17949/05_2025/8puw_17949.cif" } resolution = 3.01 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= 0.003 sd= 0.068 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 52 5.16 5 C 7134 2.51 5 N 1956 2.21 5 O 2018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11160 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1488 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 180} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 4092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4092 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 52, 'TRANS': 479} Unresolved chain links: 1 Chain breaks: 4 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 4092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4092 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 52, 'TRANS': 479} Unresolved chain links: 1 Chain breaks: 4 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1488 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 180} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 7.00, per 1000 atoms: 0.63 Number of scatterers: 11160 At special positions: 0 Unit cell: (141.075, 99.275, 89.87, 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 52 16.00 O 2018 8.00 N 1956 7.00 C 7134 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.6 seconds 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2692 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 10 sheets defined 42.2% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 removed outlier: 3.628A pdb=" N LEU A 15 " --> pdb=" O ASN A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 39 through 64 Processing helix chain 'A' and resid 67 through 86 removed outlier: 3.643A pdb=" N GLN A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 116 Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 134 through 147 removed outlier: 4.022A pdb=" N VAL A 138 " --> pdb=" O PRO A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 170 Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.561A pdb=" N LEU A 174 " --> pdb=" O TRP A 171 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY A 175 " --> pdb=" O LYS A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 171 through 175' Processing helix chain 'B' and resid 196 through 203 removed outlier: 3.723A pdb=" N LEU B 200 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 207 through 212 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 242 through 259 Processing helix chain 'B' and resid 273 through 288 Processing helix chain 'B' and resid 363 through 366 removed outlier: 4.121A pdb=" N LEU B 366 " --> pdb=" O THR B 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 363 through 366' Processing helix chain 'B' and resid 367 through 387 removed outlier: 3.562A pdb=" N PHE B 371 " --> pdb=" O ASP B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 417 removed outlier: 3.669A pdb=" N ASP B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 444 removed outlier: 3.889A pdb=" N SER B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER B 444 " --> pdb=" O CYS B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 484 Processing helix chain 'B' and resid 538 through 544 Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 654 through 661 removed outlier: 3.652A pdb=" N PHE B 661 " --> pdb=" O VAL B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 664 No H-bonds generated for 'chain 'B' and resid 662 through 664' Processing helix chain 'B' and resid 676 through 692 removed outlier: 3.818A pdb=" N TYR B 680 " --> pdb=" O PRO B 676 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 681 " --> pdb=" O THR B 677 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLY B 683 " --> pdb=" O ALA B 679 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LEU B 684 " --> pdb=" O TYR B 680 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 203 removed outlier: 3.688A pdb=" N LEU E 200 " --> pdb=" O THR E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 206 No H-bonds generated for 'chain 'E' and resid 204 through 206' Processing helix chain 'E' and resid 207 through 211 Processing helix chain 'E' and resid 226 through 230 Processing helix chain 'E' and resid 242 through 259 Processing helix chain 'E' and resid 273 through 288 Processing helix chain 'E' and resid 363 through 366 removed outlier: 4.120A pdb=" N LEU E 366 " --> pdb=" O THR E 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 363 through 366' Processing helix chain 'E' and resid 367 through 387 removed outlier: 3.563A pdb=" N PHE E 371 " --> pdb=" O ASP E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 417 removed outlier: 3.601A pdb=" N ASP E 407 " --> pdb=" O GLY E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 444 removed outlier: 3.891A pdb=" N SER E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER E 444 " --> pdb=" O CYS E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 484 Processing helix chain 'E' and resid 538 through 544 Processing helix chain 'E' and resid 555 through 560 Processing helix chain 'E' and resid 654 through 661 removed outlier: 3.644A pdb=" N PHE E 661 " --> pdb=" O VAL E 657 " (cutoff:3.500A) Processing helix chain 'E' and resid 676 through 692 removed outlier: 3.820A pdb=" N TYR E 680 " --> pdb=" O PRO E 676 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL E 681 " --> pdb=" O THR E 677 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLY E 683 " --> pdb=" O ALA E 679 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU E 684 " --> pdb=" O TYR E 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 23 removed outlier: 3.628A pdb=" N LEU D 15 " --> pdb=" O ASN D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 28 Processing helix chain 'D' and resid 39 through 64 Processing helix chain 'D' and resid 67 through 86 removed outlier: 3.647A pdb=" N GLN D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 116 Processing helix chain 'D' and resid 123 through 132 Processing helix chain 'D' and resid 134 through 147 removed outlier: 4.053A pdb=" N VAL D 138 " --> pdb=" O PRO D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 170 Processing helix chain 'D' and resid 171 through 175 removed outlier: 3.559A pdb=" N LEU D 174 " --> pdb=" O TRP D 171 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY D 175 " --> pdb=" O LYS D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 171 through 175' Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 349 removed outlier: 6.912A pdb=" N GLU B 646 " --> pdb=" O VAL B 638 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N VAL B 638 " --> pdb=" O GLU B 646 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N HIS B 648 " --> pdb=" O ARG B 636 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LEU B 629 " --> pdb=" O ARG B 552 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ARG B 552 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY B 631 " --> pdb=" O LEU B 550 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE B 527 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 121 through 124 removed outlier: 6.310A pdb=" N VAL B 188 " --> pdb=" O HIS B 150 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA5, first strand: chain 'B' and resid 351 through 358 removed outlier: 6.719A pdb=" N LEU B 320 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N MET B 356 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 318 " --> pdb=" O MET B 356 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N MET B 301 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ASN B 396 " --> pdb=" O MET B 301 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU B 303 " --> pdb=" O ASN B 396 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU B 264 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL B 421 " --> pdb=" O THR B 449 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 121 through 124 removed outlier: 6.325A pdb=" N VAL E 188 " --> pdb=" O HIS E 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 159 through 161 Processing sheet with id=AA8, first strand: chain 'E' and resid 351 through 358 removed outlier: 6.789A pdb=" N LEU E 320 " --> pdb=" O VAL E 354 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N MET E 356 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL E 318 " --> pdb=" O MET E 356 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N MET E 301 " --> pdb=" O VAL E 394 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ASN E 396 " --> pdb=" O MET E 301 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU E 303 " --> pdb=" O ASN E 396 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU E 264 " --> pdb=" O VAL E 395 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL E 421 " --> pdb=" O THR E 449 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 613 through 614 removed outlier: 6.030A pdb=" N ILE E 527 " --> pdb=" O ILE E 614 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY E 631 " --> pdb=" O LEU E 550 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ARG E 552 " --> pdb=" O LEU E 629 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LEU E 629 " --> pdb=" O ARG E 552 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N HIS E 648 " --> pdb=" O ARG E 636 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N VAL E 638 " --> pdb=" O GLU E 646 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLU E 646 " --> pdb=" O VAL E 638 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 723 through 725 525 hydrogen bonds defined for protein. 1476 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: 3.62 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3617 1.34 - 1.46: 1842 1.46 - 1.57: 5923 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 11466 Sorted by residual: bond pdb=" N GLY E 291 " pdb=" CA GLY E 291 " ideal model delta sigma weight residual 1.464 1.446 0.018 1.12e-02 7.97e+03 2.57e+00 bond pdb=" N GLY B 291 " pdb=" CA GLY B 291 " ideal model delta sigma weight residual 1.464 1.447 0.018 1.12e-02 7.97e+03 2.45e+00 bond pdb=" CB GLN A 3 " pdb=" CG GLN A 3 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.91e+00 bond pdb=" CA GLY B 291 " pdb=" C GLY B 291 " ideal model delta sigma weight residual 1.530 1.516 0.014 1.04e-02 9.25e+03 1.88e+00 bond pdb=" CB GLN D 3 " pdb=" CG GLN D 3 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.86e+00 ... (remaining 11461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 14969 1.50 - 3.01: 567 3.01 - 4.51: 89 4.51 - 6.01: 21 6.01 - 7.51: 6 Bond angle restraints: 15652 Sorted by residual: angle pdb=" C TYR E 530 " pdb=" N ASP E 531 " pdb=" CA ASP E 531 " ideal model delta sigma weight residual 121.54 129.05 -7.51 1.91e+00 2.74e-01 1.55e+01 angle pdb=" C TYR B 530 " pdb=" N ASP B 531 " pdb=" CA ASP B 531 " ideal model delta sigma weight residual 121.54 128.99 -7.45 1.91e+00 2.74e-01 1.52e+01 angle pdb=" C ILE B 359 " pdb=" N ALA B 360 " pdb=" CA ALA B 360 " ideal model delta sigma weight residual 122.40 127.54 -5.14 1.45e+00 4.76e-01 1.26e+01 angle pdb=" C ILE E 359 " pdb=" N ALA E 360 " pdb=" CA ALA E 360 " ideal model delta sigma weight residual 122.40 127.52 -5.12 1.45e+00 4.76e-01 1.25e+01 angle pdb=" CB GLN D 3 " pdb=" CG GLN D 3 " pdb=" CD GLN D 3 " ideal model delta sigma weight residual 112.60 118.18 -5.58 1.70e+00 3.46e-01 1.08e+01 ... (remaining 15647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 6357 17.84 - 35.68: 404 35.68 - 53.52: 59 53.52 - 71.36: 16 71.36 - 89.20: 6 Dihedral angle restraints: 6842 sinusoidal: 2688 harmonic: 4154 Sorted by residual: dihedral pdb=" CA TYR E 423 " pdb=" C TYR E 423 " pdb=" N MET E 424 " pdb=" CA MET E 424 " ideal model delta harmonic sigma weight residual -180.00 -161.55 -18.45 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA TYR B 423 " pdb=" C TYR B 423 " pdb=" N MET B 424 " pdb=" CA MET B 424 " ideal model delta harmonic sigma weight residual -180.00 -161.58 -18.42 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA MET E 286 " pdb=" C MET E 286 " pdb=" N THR E 287 " pdb=" CA THR E 287 " ideal model delta harmonic sigma weight residual -180.00 -162.96 -17.04 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 6839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1303 0.040 - 0.080: 302 0.080 - 0.121: 125 0.121 - 0.161: 20 0.161 - 0.201: 4 Chirality restraints: 1754 Sorted by residual: chirality pdb=" CB ILE E 156 " pdb=" CA ILE E 156 " pdb=" CG1 ILE E 156 " pdb=" CG2 ILE E 156 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE B 156 " pdb=" CA ILE B 156 " pdb=" CG1 ILE B 156 " pdb=" CG2 ILE B 156 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CG LEU B 280 " pdb=" CB LEU B 280 " pdb=" CD1 LEU B 280 " pdb=" CD2 LEU B 280 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.06e-01 ... (remaining 1751 not shown) Planarity restraints: 2012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 115 " 0.039 5.00e-02 4.00e+02 5.98e-02 5.71e+00 pdb=" N PRO B 116 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 116 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 116 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN E 115 " 0.038 5.00e-02 4.00e+02 5.82e-02 5.43e+00 pdb=" N PRO E 116 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO E 116 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 116 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 94 " -0.024 2.00e-02 2.50e+03 1.52e-02 4.65e+00 pdb=" CG TYR D 94 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR D 94 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR D 94 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR D 94 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR D 94 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR D 94 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 94 " -0.006 2.00e-02 2.50e+03 ... (remaining 2009 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2666 2.80 - 3.33: 10052 3.33 - 3.85: 18567 3.85 - 4.38: 22105 4.38 - 4.90: 38220 Nonbonded interactions: 91610 Sorted by model distance: nonbonded pdb=" OE1 GLU A 139 " pdb=" OG1 THR E 404 " model vdw 2.276 3.040 nonbonded pdb=" NE2 HIS E 174 " pdb=" O ARG E 212 " model vdw 2.291 3.120 nonbonded pdb=" NE2 HIS B 174 " pdb=" O ARG B 212 " model vdw 2.300 3.120 nonbonded pdb=" O GLY B 545 " pdb=" OH TYR B 680 " model vdw 2.385 3.040 nonbonded pdb=" O GLY E 545 " pdb=" OH TYR E 680 " model vdw 2.394 3.040 ... (remaining 91605 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 28.370 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 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 : 0.004 0.041 11466 Z= 0.185 Angle : 0.693 7.514 15652 Z= 0.391 Chirality : 0.043 0.201 1754 Planarity : 0.008 0.067 2012 Dihedral : 12.229 89.202 4150 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: 0.73 (0.21), residues: 1406 helix: 1.09 (0.20), residues: 496 sheet: -0.09 (0.37), residues: 196 loop : 0.37 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 214 HIS 0.006 0.001 HIS B 174 PHE 0.021 0.002 PHE D 22 TYR 0.034 0.002 TYR D 94 ARG 0.016 0.001 ARG E 560 Details of bonding type rmsd hydrogen bonds : bond 0.13705 ( 525) hydrogen bonds : angle 6.24437 ( 1476) covalent geometry : bond 0.00399 (11466) covalent geometry : angle 0.69345 (15652) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 1.235 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2738 time to fit residues: 37.8030 Evaluate side-chains 84 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS B 144 ASN E 144 ASN D 146 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.111144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.085187 restraints weight = 15467.846| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.22 r_work: 0.2790 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11466 Z= 0.163 Angle : 0.533 9.987 15652 Z= 0.267 Chirality : 0.041 0.132 1754 Planarity : 0.006 0.042 2012 Dihedral : 4.215 24.099 1554 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.34 % Allowed : 4.52 % Favored : 95.14 % 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 (0.22), residues: 1406 helix: 2.08 (0.22), residues: 506 sheet: 0.17 (0.39), residues: 178 loop : 0.71 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 214 HIS 0.009 0.001 HIS E 174 PHE 0.016 0.002 PHE D 107 TYR 0.016 0.002 TYR A 94 ARG 0.007 0.001 ARG E 560 Details of bonding type rmsd hydrogen bonds : bond 0.04529 ( 525) hydrogen bonds : angle 4.72152 ( 1476) covalent geometry : bond 0.00390 (11466) covalent geometry : angle 0.53292 (15652) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 1.229 Fit side-chains REVERT: B 186 ASP cc_start: 0.8138 (t0) cc_final: 0.7787 (t0) REVERT: B 259 LYS cc_start: 0.7464 (mtmt) cc_final: 0.6798 (ptpt) REVERT: E 259 LYS cc_start: 0.7463 (mtmt) cc_final: 0.6801 (ptpt) outliers start: 4 outliers final: 2 residues processed: 98 average time/residue: 0.2638 time to fit residues: 36.5339 Evaluate side-chains 89 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain E residue 427 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 14 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 118 optimal weight: 0.0170 chunk 47 optimal weight: 1.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.111028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.084961 restraints weight = 15689.905| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.23 r_work: 0.2783 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11466 Z= 0.133 Angle : 0.486 6.821 15652 Z= 0.241 Chirality : 0.040 0.134 1754 Planarity : 0.005 0.036 2012 Dihedral : 3.998 20.783 1554 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.75 % Allowed : 6.62 % Favored : 92.63 % 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: 1.87 (0.22), residues: 1406 helix: 2.51 (0.22), residues: 506 sheet: 0.11 (0.39), residues: 178 loop : 0.75 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 214 HIS 0.007 0.001 HIS E 174 PHE 0.013 0.002 PHE D 107 TYR 0.010 0.001 TYR A 94 ARG 0.003 0.000 ARG D 106 Details of bonding type rmsd hydrogen bonds : bond 0.04001 ( 525) hydrogen bonds : angle 4.44814 ( 1476) covalent geometry : bond 0.00318 (11466) covalent geometry : angle 0.48606 (15652) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 1.233 Fit side-chains REVERT: A 94 TYR cc_start: 0.9121 (OUTLIER) cc_final: 0.8087 (m-10) REVERT: B 186 ASP cc_start: 0.8155 (t0) cc_final: 0.7763 (t0) REVERT: B 259 LYS cc_start: 0.7491 (mtmt) cc_final: 0.6874 (ptpt) REVERT: E 186 ASP cc_start: 0.8142 (t0) cc_final: 0.7866 (t0) REVERT: E 259 LYS cc_start: 0.7504 (mtmt) cc_final: 0.6886 (ptpt) REVERT: D 94 TYR cc_start: 0.9129 (OUTLIER) cc_final: 0.8087 (m-10) outliers start: 9 outliers final: 4 residues processed: 103 average time/residue: 0.2643 time to fit residues: 38.4752 Evaluate side-chains 93 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain D residue 94 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 17 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 94 optimal weight: 0.0870 chunk 137 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.106559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.080311 restraints weight = 15793.321| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.23 r_work: 0.2727 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 11466 Z= 0.310 Angle : 0.616 5.845 15652 Z= 0.304 Chirality : 0.045 0.135 1754 Planarity : 0.006 0.038 2012 Dihedral : 4.354 20.575 1554 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.59 % Allowed : 7.04 % Favored : 92.38 % 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: 1.53 (0.22), residues: 1406 helix: 2.16 (0.22), residues: 506 sheet: 0.07 (0.34), residues: 232 loop : 0.61 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 168 HIS 0.008 0.002 HIS E 174 PHE 0.018 0.002 PHE D 107 TYR 0.018 0.002 TYR A 94 ARG 0.007 0.001 ARG D 106 Details of bonding type rmsd hydrogen bonds : bond 0.05231 ( 525) hydrogen bonds : angle 4.60089 ( 1476) covalent geometry : bond 0.00766 (11466) covalent geometry : angle 0.61557 (15652) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 1.198 Fit side-chains REVERT: A 94 TYR cc_start: 0.9250 (OUTLIER) cc_final: 0.8076 (m-10) REVERT: B 186 ASP cc_start: 0.8147 (t0) cc_final: 0.7883 (t0) REVERT: B 259 LYS cc_start: 0.7598 (mtmt) cc_final: 0.7182 (ptpp) REVERT: E 259 LYS cc_start: 0.7597 (mtmt) cc_final: 0.7180 (ptpp) REVERT: D 94 TYR cc_start: 0.9262 (OUTLIER) cc_final: 0.8197 (m-10) outliers start: 7 outliers final: 3 residues processed: 92 average time/residue: 0.2625 time to fit residues: 34.8206 Evaluate side-chains 90 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain D residue 94 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 120 optimal weight: 0.4980 chunk 18 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.109460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.083433 restraints weight = 15565.761| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.08 r_work: 0.2779 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11466 Z= 0.131 Angle : 0.482 4.634 15652 Z= 0.241 Chirality : 0.040 0.135 1754 Planarity : 0.005 0.036 2012 Dihedral : 4.053 20.425 1554 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.09 % Allowed : 7.20 % Favored : 91.71 % 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: 1.79 (0.22), residues: 1406 helix: 2.60 (0.22), residues: 506 sheet: -0.13 (0.38), residues: 178 loop : 0.62 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 214 HIS 0.003 0.001 HIS E 174 PHE 0.012 0.001 PHE A 104 TYR 0.010 0.001 TYR D 100 ARG 0.004 0.000 ARG D 106 Details of bonding type rmsd hydrogen bonds : bond 0.03946 ( 525) hydrogen bonds : angle 4.40827 ( 1476) covalent geometry : bond 0.00317 (11466) covalent geometry : angle 0.48222 (15652) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 1.223 Fit side-chains REVERT: A 94 TYR cc_start: 0.9128 (OUTLIER) cc_final: 0.8041 (m-10) REVERT: B 259 LYS cc_start: 0.7528 (mtmt) cc_final: 0.6947 (ptpt) REVERT: E 259 LYS cc_start: 0.7532 (mtmt) cc_final: 0.7088 (ptpp) REVERT: D 94 TYR cc_start: 0.9130 (OUTLIER) cc_final: 0.8043 (m-10) outliers start: 13 outliers final: 8 residues processed: 107 average time/residue: 0.2505 time to fit residues: 38.0109 Evaluate side-chains 106 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 356 MET Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 116 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 80 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 136 optimal weight: 0.7980 chunk 116 optimal weight: 0.0980 chunk 90 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.109611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.083557 restraints weight = 15682.173| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.09 r_work: 0.2794 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11466 Z= 0.136 Angle : 0.491 5.213 15652 Z= 0.243 Chirality : 0.040 0.149 1754 Planarity : 0.005 0.034 2012 Dihedral : 3.980 20.027 1554 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.01 % Allowed : 7.45 % Favored : 91.54 % 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: 1.86 (0.22), residues: 1406 helix: 2.72 (0.22), residues: 506 sheet: -0.19 (0.38), residues: 178 loop : 0.65 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 214 HIS 0.003 0.001 HIS E 174 PHE 0.012 0.001 PHE A 104 TYR 0.011 0.001 TYR D 100 ARG 0.003 0.000 ARG D 106 Details of bonding type rmsd hydrogen bonds : bond 0.03941 ( 525) hydrogen bonds : angle 4.37988 ( 1476) covalent geometry : bond 0.00328 (11466) covalent geometry : angle 0.49122 (15652) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 1.315 Fit side-chains REVERT: A 94 TYR cc_start: 0.9124 (OUTLIER) cc_final: 0.8013 (m-10) REVERT: B 259 LYS cc_start: 0.7533 (mtmt) cc_final: 0.7112 (ptpp) REVERT: E 259 LYS cc_start: 0.7540 (mtmt) cc_final: 0.7117 (ptpp) REVERT: D 94 TYR cc_start: 0.9124 (OUTLIER) cc_final: 0.8003 (m-10) outliers start: 12 outliers final: 8 residues processed: 100 average time/residue: 0.2763 time to fit residues: 40.2979 Evaluate side-chains 102 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 356 MET Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 116 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 57 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 91 optimal weight: 0.0870 chunk 138 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.110896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.084685 restraints weight = 15667.747| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.30 r_work: 0.2783 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11466 Z= 0.108 Angle : 0.462 4.762 15652 Z= 0.229 Chirality : 0.039 0.135 1754 Planarity : 0.005 0.034 2012 Dihedral : 3.838 19.723 1554 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.09 % Allowed : 8.04 % Favored : 90.87 % 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: 2.02 (0.22), residues: 1406 helix: 2.88 (0.22), residues: 506 sheet: -0.10 (0.38), residues: 178 loop : 0.72 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 214 HIS 0.003 0.001 HIS B 174 PHE 0.010 0.001 PHE B 265 TYR 0.009 0.001 TYR A 94 ARG 0.003 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.03552 ( 525) hydrogen bonds : angle 4.27903 ( 1476) covalent geometry : bond 0.00257 (11466) covalent geometry : angle 0.46181 (15652) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 1.379 Fit side-chains REVERT: A 94 TYR cc_start: 0.9130 (OUTLIER) cc_final: 0.8112 (m-10) REVERT: B 186 ASP cc_start: 0.8065 (t0) cc_final: 0.7724 (t0) REVERT: B 259 LYS cc_start: 0.7499 (mtmt) cc_final: 0.7092 (ptpp) REVERT: E 186 ASP cc_start: 0.8089 (t0) cc_final: 0.7705 (t0) REVERT: E 259 LYS cc_start: 0.7513 (mtmt) cc_final: 0.7102 (ptpp) REVERT: D 94 TYR cc_start: 0.9118 (OUTLIER) cc_final: 0.8106 (m-10) outliers start: 13 outliers final: 8 residues processed: 107 average time/residue: 0.2744 time to fit residues: 41.5749 Evaluate side-chains 101 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 356 MET Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 116 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 96 optimal weight: 0.8980 chunk 111 optimal weight: 0.0670 chunk 35 optimal weight: 0.5980 chunk 117 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.110278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.085084 restraints weight = 15611.574| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.08 r_work: 0.2788 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11466 Z= 0.127 Angle : 0.474 4.889 15652 Z= 0.235 Chirality : 0.040 0.135 1754 Planarity : 0.005 0.032 2012 Dihedral : 3.848 19.656 1554 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.92 % Allowed : 8.79 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.22), residues: 1406 helix: 2.91 (0.22), residues: 506 sheet: -0.13 (0.38), residues: 178 loop : 0.72 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 214 HIS 0.003 0.001 HIS B 174 PHE 0.012 0.001 PHE A 104 TYR 0.011 0.001 TYR A 94 ARG 0.003 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.03709 ( 525) hydrogen bonds : angle 4.28350 ( 1476) covalent geometry : bond 0.00307 (11466) covalent geometry : angle 0.47361 (15652) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 1.311 Fit side-chains REVERT: A 94 TYR cc_start: 0.9144 (OUTLIER) cc_final: 0.8149 (m-10) REVERT: B 259 LYS cc_start: 0.7517 (mtmt) cc_final: 0.7136 (ptpp) REVERT: E 186 ASP cc_start: 0.8055 (t0) cc_final: 0.7675 (t0) REVERT: E 259 LYS cc_start: 0.7543 (mtmt) cc_final: 0.7157 (ptpp) REVERT: D 94 TYR cc_start: 0.9148 (OUTLIER) cc_final: 0.8155 (m-10) outliers start: 11 outliers final: 9 residues processed: 101 average time/residue: 0.2368 time to fit residues: 34.8557 Evaluate side-chains 102 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 356 MET Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 116 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 23 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.109156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.083862 restraints weight = 15633.496| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.08 r_work: 0.2768 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11466 Z= 0.158 Angle : 0.494 4.939 15652 Z= 0.245 Chirality : 0.041 0.138 1754 Planarity : 0.005 0.032 2012 Dihedral : 3.926 19.587 1554 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.84 % Allowed : 9.05 % Favored : 90.12 % 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 (0.22), residues: 1406 helix: 2.86 (0.22), residues: 506 sheet: -0.16 (0.38), residues: 178 loop : 0.69 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 168 HIS 0.004 0.001 HIS B 174 PHE 0.014 0.002 PHE A 104 TYR 0.013 0.001 TYR A 94 ARG 0.003 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.03991 ( 525) hydrogen bonds : angle 4.32175 ( 1476) covalent geometry : bond 0.00386 (11466) covalent geometry : angle 0.49427 (15652) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 1.330 Fit side-chains REVERT: A 94 TYR cc_start: 0.9159 (OUTLIER) cc_final: 0.8056 (m-10) REVERT: B 259 LYS cc_start: 0.7590 (mtmt) cc_final: 0.7027 (ptpt) REVERT: E 186 ASP cc_start: 0.8087 (t0) cc_final: 0.7705 (t0) REVERT: E 259 LYS cc_start: 0.7583 (mtmt) cc_final: 0.7021 (ptpt) REVERT: D 94 TYR cc_start: 0.9164 (OUTLIER) cc_final: 0.8066 (m-10) outliers start: 10 outliers final: 7 residues processed: 98 average time/residue: 0.2719 time to fit residues: 38.1989 Evaluate side-chains 99 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 356 MET Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 116 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 38 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 140 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.109852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.084666 restraints weight = 15652.822| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.09 r_work: 0.2782 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11466 Z= 0.130 Angle : 0.476 4.861 15652 Z= 0.236 Chirality : 0.040 0.134 1754 Planarity : 0.005 0.032 2012 Dihedral : 3.859 19.694 1554 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.92 % Allowed : 9.05 % Favored : 90.03 % 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: 2.04 (0.22), residues: 1406 helix: 2.91 (0.22), residues: 506 sheet: -0.13 (0.39), residues: 178 loop : 0.73 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 214 HIS 0.003 0.001 HIS B 174 PHE 0.012 0.001 PHE A 104 TYR 0.011 0.001 TYR A 94 ARG 0.003 0.000 ARG D 106 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 525) hydrogen bonds : angle 4.28651 ( 1476) covalent geometry : bond 0.00316 (11466) covalent geometry : angle 0.47585 (15652) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2812 Ramachandran restraints generated. 1406 Oldfield, 0 Emsley, 1406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 1.276 Fit side-chains revert: symmetry clash REVERT: A 94 TYR cc_start: 0.9169 (OUTLIER) cc_final: 0.8183 (m-10) REVERT: B 259 LYS cc_start: 0.7552 (mtmt) cc_final: 0.6983 (ptpt) REVERT: E 186 ASP cc_start: 0.8076 (t0) cc_final: 0.7709 (t0) REVERT: E 259 LYS cc_start: 0.7554 (mtmt) cc_final: 0.6984 (ptpt) REVERT: D 94 TYR cc_start: 0.9174 (OUTLIER) cc_final: 0.8187 (m-10) outliers start: 11 outliers final: 8 residues processed: 98 average time/residue: 0.2596 time to fit residues: 36.1675 Evaluate side-chains 96 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 356 MET Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 116 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 116 optimal weight: 0.0470 chunk 1 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 55 optimal weight: 0.0970 chunk 108 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 115 optimal weight: 0.0670 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 overall best weight: 0.2814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.111995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.087353 restraints weight = 15495.031| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.07 r_work: 0.2811 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11466 Z= 0.090 Angle : 0.445 4.772 15652 Z= 0.222 Chirality : 0.039 0.135 1754 Planarity : 0.004 0.034 2012 Dihedral : 3.674 19.582 1554 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.92 % Allowed : 8.88 % Favored : 90.20 % 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: 2.23 (0.23), residues: 1406 helix: 3.08 (0.22), residues: 506 sheet: 0.02 (0.39), residues: 178 loop : 0.81 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 214 HIS 0.002 0.000 HIS B 174 PHE 0.008 0.001 PHE E 265 TYR 0.008 0.001 TYR A 94 ARG 0.003 0.000 ARG E 417 Details of bonding type rmsd hydrogen bonds : bond 0.03209 ( 525) hydrogen bonds : angle 4.18035 ( 1476) covalent geometry : bond 0.00210 (11466) covalent geometry : angle 0.44532 (15652) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5651.59 seconds wall clock time: 98 minutes 28.56 seconds (5908.56 seconds total)