Starting phenix.real_space_refine on Sat Nov 16 13:17:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8puw_17949/11_2024/8puw_17949.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8puw_17949/11_2024/8puw_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8puw_17949/11_2024/8puw_17949.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8puw_17949/11_2024/8puw_17949.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8puw_17949/11_2024/8puw_17949.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8puw_17949/11_2024/8puw_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 7.15, per 1000 atoms: 0.64 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: 2.58 Conformation dependent library (CDL) restraints added in 1.5 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: 1.33 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: 3.80 Time building geometry restraints manager: 3.02 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: 0.00 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: 1.380 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.430 Find NCS groups from input model: 0.290 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.420 ------------------------------------------------------------------------------- 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= 0.262 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 *********************** 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 : 1.337 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2854 time to fit residues: 39.2304 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 : 1.286 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 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= 0.260 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 *********************** 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 : 1.142 Fit side-chains REVERT: B 186 ASP cc_start: 0.7498 (t0) cc_final: 0.7230 (t0) REVERT: B 259 LYS cc_start: 0.7393 (mtmt) cc_final: 0.6820 (ptpt) REVERT: E 259 LYS cc_start: 0.7397 (mtmt) cc_final: 0.6824 (ptpt) outliers start: 4 outliers final: 2 residues processed: 98 average time/residue: 0.2676 time to fit residues: 36.7417 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 : 1.254 ------------------------------------------------------------------------------- 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 40 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 139 optimal weight: 0.7980 chunk 115 optimal weight: 0.0870 chunk 128 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 103 optimal weight: 0.0870 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1060 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= 0.158 Angle : 0.463 7.209 15652 Z= 0.229 Chirality : 0.039 0.135 1754 Planarity : 0.005 0.036 2012 Dihedral : 3.905 20.909 1554 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.84 % Allowed : 6.28 % Favored : 92.88 % 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: 1.96 (0.22), residues: 1406 helix: 2.59 (0.22), residues: 506 sheet: 0.17 (0.39), residues: 178 loop : 0.79 (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 0.011 0.001 PHE D 107 TYR 0.009 0.001 TYR A 94 ARG 0.005 0.000 ARG E 560 *********************** 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 109 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 1.307 Fit side-chains REVERT: A 94 TYR cc_start: 0.8819 (OUTLIER) cc_final: 0.7762 (m-80) REVERT: B 186 ASP cc_start: 0.7538 (t0) cc_final: 0.7244 (t0) REVERT: B 259 LYS cc_start: 0.7376 (mtmt) cc_final: 0.6832 (ptpt) REVERT: E 259 LYS cc_start: 0.7380 (mtmt) cc_final: 0.6835 (ptpt) REVERT: D 94 TYR cc_start: 0.8832 (OUTLIER) cc_final: 0.7775 (m-80) outliers start: 10 outliers final: 6 residues processed: 105 average time/residue: 0.2688 time to fit residues: 39.9400 Evaluate side-chains 96 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 427 ASP Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 116 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 61 optimal weight: 0.1980 chunk 86 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 137 optimal weight: 0.0980 chunk 122 optimal weight: 0.6980 chunk 36 optimal weight: 0.0030 chunk 114 optimal weight: 0.0020 overall best weight: 0.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1276 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= 0.122 Angle : 0.436 4.610 15652 Z= 0.215 Chirality : 0.038 0.138 1754 Planarity : 0.005 0.036 2012 Dihedral : 3.676 19.529 1554 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % 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: 2.19 (0.22), residues: 1406 helix: 2.92 (0.22), residues: 506 sheet: 0.29 (0.40), residues: 178 loop : 0.81 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 511 HIS 0.004 0.000 HIS E 174 PHE 0.010 0.001 PHE B 265 TYR 0.007 0.001 TYR D 100 ARG 0.002 0.000 ARG B 201 *********************** 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 108 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 1.385 Fit side-chains REVERT: A 94 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.7729 (m-80) REVERT: B 259 LYS cc_start: 0.7416 (mtmt) cc_final: 0.6915 (ptpt) REVERT: E 259 LYS cc_start: 0.7416 (mtmt) cc_final: 0.6916 (ptpt) REVERT: D 94 TYR cc_start: 0.8728 (OUTLIER) cc_final: 0.7742 (m-80) outliers start: 7 outliers final: 3 residues processed: 106 average time/residue: 0.2707 time to fit residues: 39.8818 Evaluate side-chains 94 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 1.950 ------------------------------------------------------------------------------- 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 354 GLU Chi-restraints excluded: chain E residue 164 ILE 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 77 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 70 optimal weight: 0.0870 chunk 123 optimal weight: 0.0170 chunk 34 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1302 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= 0.236 Angle : 0.505 12.822 15652 Z= 0.244 Chirality : 0.040 0.134 1754 Planarity : 0.005 0.033 2012 Dihedral : 3.815 19.341 1554 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.84 % Allowed : 7.62 % 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: 2.14 (0.22), residues: 1406 helix: 2.90 (0.22), residues: 506 sheet: 0.19 (0.40), residues: 178 loop : 0.78 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 168 HIS 0.006 0.001 HIS E 174 PHE 0.014 0.002 PHE D 107 TYR 0.012 0.001 TYR A 94 ARG 0.004 0.000 ARG D 106 *********************** 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 101 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 1.304 Fit side-chains REVERT: A 94 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.7876 (m-10) REVERT: B 259 LYS cc_start: 0.7486 (mtmt) cc_final: 0.7196 (ptpp) REVERT: E 259 LYS cc_start: 0.7485 (mtmt) cc_final: 0.7198 (ptpp) REVERT: D 94 TYR cc_start: 0.8932 (OUTLIER) cc_final: 0.7890 (m-10) outliers start: 10 outliers final: 6 residues processed: 97 average time/residue: 0.2939 time to fit residues: 41.7374 Evaluate side-chains 95 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 1.448 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 0.2980 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 137 optimal weight: 0.7980 chunk 114 optimal weight: 0.0020 chunk 63 optimal weight: 0.0570 chunk 11 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.3906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1391 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= 0.155 Angle : 0.451 5.943 15652 Z= 0.223 Chirality : 0.039 0.136 1754 Planarity : 0.004 0.033 2012 Dihedral : 3.711 19.137 1554 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % 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: 2.23 (0.22), residues: 1406 helix: 3.06 (0.22), residues: 506 sheet: 0.18 (0.40), residues: 178 loop : 0.78 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 214 HIS 0.004 0.001 HIS E 174 PHE 0.010 0.001 PHE B 265 TYR 0.008 0.001 TYR A 94 ARG 0.003 0.000 ARG D 106 *********************** 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 108 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 1.377 Fit side-chains REVERT: A 94 TYR cc_start: 0.8850 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: B 186 ASP cc_start: 0.7382 (t0) cc_final: 0.7084 (t0) REVERT: B 259 LYS cc_start: 0.7463 (mtmt) cc_final: 0.7176 (ptpp) REVERT: E 259 LYS cc_start: 0.7470 (mtmt) cc_final: 0.7184 (ptpp) REVERT: D 94 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.7810 (m-80) outliers start: 12 outliers final: 8 residues processed: 105 average time/residue: 0.2686 time to fit residues: 40.4058 Evaluate side-chains 95 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 1.306 ------------------------------------------------------------------------------- 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 226 THR 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 15 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 77 optimal weight: 0.0980 chunk 115 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11466 Z= 0.231 Angle : 0.485 5.183 15652 Z= 0.240 Chirality : 0.040 0.133 1754 Planarity : 0.005 0.032 2012 Dihedral : 3.827 19.384 1554 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.01 % Allowed : 7.96 % Favored : 91.04 % 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: 2.17 (0.22), residues: 1406 helix: 3.00 (0.22), residues: 506 sheet: 0.11 (0.39), residues: 178 loop : 0.77 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 168 HIS 0.005 0.001 HIS E 174 PHE 0.014 0.002 PHE A 104 TYR 0.012 0.001 TYR A 94 ARG 0.004 0.000 ARG D 106 *********************** 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 107 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 1.326 Fit side-chains REVERT: A 94 TYR cc_start: 0.8978 (OUTLIER) cc_final: 0.7817 (m-10) REVERT: B 186 ASP cc_start: 0.7469 (t0) cc_final: 0.7201 (t0) REVERT: B 259 LYS cc_start: 0.7504 (mtmt) cc_final: 0.7254 (ptpp) REVERT: E 259 LYS cc_start: 0.7532 (mtmt) cc_final: 0.7285 (ptpp) REVERT: D 94 TYR cc_start: 0.8991 (OUTLIER) cc_final: 0.7951 (m-10) outliers start: 12 outliers final: 8 residues processed: 104 average time/residue: 0.2384 time to fit residues: 35.9961 Evaluate side-chains 108 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 1.401 ------------------------------------------------------------------------------- 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 226 THR 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 54 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 93 optimal weight: 0.0970 chunk 67 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11466 Z= 0.181 Angle : 0.465 4.807 15652 Z= 0.231 Chirality : 0.039 0.134 1754 Planarity : 0.004 0.032 2012 Dihedral : 3.756 19.597 1554 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.84 % Allowed : 8.38 % Favored : 90.79 % 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: 2.19 (0.22), residues: 1406 helix: 3.03 (0.22), residues: 506 sheet: 0.10 (0.39), residues: 178 loop : 0.78 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 214 HIS 0.003 0.001 HIS E 174 PHE 0.011 0.001 PHE A 104 TYR 0.010 0.001 TYR A 94 ARG 0.003 0.000 ARG D 106 *********************** 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 111 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 1.410 Fit side-chains REVERT: A 94 TYR cc_start: 0.8931 (OUTLIER) cc_final: 0.7858 (m-10) REVERT: B 186 ASP cc_start: 0.7451 (t0) cc_final: 0.7211 (t0) REVERT: B 259 LYS cc_start: 0.7505 (mtmt) cc_final: 0.7261 (ptpp) REVERT: E 259 LYS cc_start: 0.7510 (mtmt) cc_final: 0.7265 (ptpp) REVERT: D 94 TYR cc_start: 0.8945 (OUTLIER) cc_final: 0.7874 (m-10) outliers start: 10 outliers final: 8 residues processed: 108 average time/residue: 0.2728 time to fit residues: 41.7984 Evaluate side-chains 108 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 226 THR 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 119 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 76 optimal weight: 0.0980 chunk 55 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 115 optimal weight: 0.2980 chunk 120 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 644 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11466 Z= 0.203 Angle : 0.472 4.903 15652 Z= 0.234 Chirality : 0.040 0.133 1754 Planarity : 0.004 0.032 2012 Dihedral : 3.777 19.657 1554 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.84 % Allowed : 8.38 % Favored : 90.79 % 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: 2.18 (0.22), residues: 1406 helix: 3.00 (0.22), residues: 506 sheet: 0.12 (0.39), residues: 178 loop : 0.78 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 214 HIS 0.003 0.001 HIS B 174 PHE 0.012 0.001 PHE D 104 TYR 0.011 0.001 TYR A 94 ARG 0.003 0.000 ARG D 106 *********************** 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 105 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 1.168 Fit side-chains REVERT: A 94 TYR cc_start: 0.8961 (OUTLIER) cc_final: 0.7886 (m-10) REVERT: B 186 ASP cc_start: 0.7496 (t0) cc_final: 0.7241 (t0) REVERT: B 259 LYS cc_start: 0.7497 (mtmt) cc_final: 0.7039 (ptpt) REVERT: E 259 LYS cc_start: 0.7518 (mtmt) cc_final: 0.7068 (ptpt) REVERT: D 94 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.7897 (m-10) outliers start: 10 outliers final: 8 residues processed: 102 average time/residue: 0.2493 time to fit residues: 36.8728 Evaluate side-chains 104 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 1.305 ------------------------------------------------------------------------------- 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 226 THR 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 82 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 309 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11466 Z= 0.234 Angle : 0.488 4.961 15652 Z= 0.242 Chirality : 0.040 0.133 1754 Planarity : 0.005 0.031 2012 Dihedral : 3.844 19.667 1554 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.92 % Allowed : 8.46 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.22), residues: 1406 helix: 2.94 (0.22), residues: 506 sheet: 0.02 (0.39), residues: 178 loop : 0.76 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 168 HIS 0.004 0.001 HIS E 484 PHE 0.014 0.002 PHE A 104 TYR 0.012 0.001 TYR A 94 ARG 0.004 0.000 ARG D 106 ********************** 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 106 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 1.382 Fit side-chains REVERT: A 94 TYR cc_start: 0.9015 (OUTLIER) cc_final: 0.7833 (m-10) REVERT: B 259 LYS cc_start: 0.7553 (mtmt) cc_final: 0.7130 (ptpt) REVERT: E 259 LYS cc_start: 0.7551 (mtmt) cc_final: 0.7131 (ptpt) REVERT: D 94 TYR cc_start: 0.9028 (OUTLIER) cc_final: 0.7978 (m-10) outliers start: 11 outliers final: 9 residues processed: 102 average time/residue: 0.2797 time to fit residues: 40.1491 Evaluate side-chains 104 residues out of total 1220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 354 GLU 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 226 THR 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 34 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 115 optimal weight: 0.0170 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.7622 ------------------------------------------------------------------------------- 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 = 0.3330 r_free = 0.3330 target = 0.109880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.083921 restraints weight = 15518.390| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.07 r_work: 0.2786 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1603 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= 0.236 Angle : 0.489 4.915 15652 Z= 0.244 Chirality : 0.040 0.136 1754 Planarity : 0.005 0.031 2012 Dihedral : 3.842 19.619 1554 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.92 % Allowed : 8.54 % Favored : 90.54 % 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: 2.11 (0.22), residues: 1406 helix: 2.94 (0.22), residues: 506 sheet: -0.01 (0.39), residues: 178 loop : 0.77 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 214 HIS 0.004 0.001 HIS B 174 PHE 0.013 0.002 PHE A 104 TYR 0.012 0.001 TYR A 94 ARG 0.004 0.000 ARG D 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2314.94 seconds wall clock time: 43 minutes 19.53 seconds (2599.53 seconds total)