Starting phenix.real_space_refine on Sat Jul 20 14:39:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8puw_17949/07_2024/8puw_17949.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8puw_17949/07_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_17949/07_2024/8puw_17949.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8puw_17949/07_2024/8puw_17949.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8puw_17949/07_2024/8puw_17949.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8puw_17949/07_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 Residue "A ASP 113": "OD1" <-> "OD2" Residue "A ASP 126": "OD1" <-> "OD2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A GLU 164": "OE1" <-> "OE2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 407": "OD1" <-> "OD2" Residue "B PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 718": "OD1" <-> "OD2" Residue "E ASP 186": "OD1" <-> "OD2" Residue "E PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 407": "OD1" <-> "OD2" Residue "E PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 113": "OD1" <-> "OD2" Residue "D ASP 126": "OD1" <-> "OD2" Residue "D GLU 147": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 6.85, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.10 Conformation dependent library (CDL) restraints added in 2.1 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: 1.25 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: 3.43 Time building geometry restraints manager: 4.53 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: 99.08 - 106.08: 481 106.08 - 113.08: 6284 113.08 - 120.08: 3648 120.08 - 127.08: 5002 127.08 - 134.08: 237 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 2.440 nonbonded pdb=" NE2 HIS E 174 " pdb=" O ARG E 212 " model vdw 2.291 2.520 nonbonded pdb=" NE2 HIS B 174 " pdb=" O ARG B 212 " model vdw 2.300 2.520 nonbonded pdb=" O GLY B 545 " pdb=" OH TYR B 680 " model vdw 2.385 2.440 nonbonded pdb=" O GLY E 545 " pdb=" OH TYR E 680 " model vdw 2.394 2.440 ... (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 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: 1.790 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 32.600 Find NCS groups from input model: 0.360 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.210 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.348 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2798 time to fit residues: 38.5161 Evaluate side-chains 84 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.298 ------------------------------------------------------------------------------- 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: 1.9990 chunk 107 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 0.0770 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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: 0.8513 moved from start: 0.0711 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= 0.197 Angle : 0.497 10.136 15652 Z= 0.247 Chirality : 0.039 0.133 1754 Planarity : 0.006 0.043 2012 Dihedral : 4.116 24.296 1554 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.34 % Allowed : 4.69 % Favored : 94.97 % 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: 1.69 (0.22), residues: 1406 helix: 2.21 (0.22), residues: 506 sheet: 0.12 (0.38), residues: 184 loop : 0.74 (0.24), residues: 716 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 0.013 0.002 PHE D 107 TYR 0.014 0.001 TYR D 94 ARG 0.005 0.000 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 94 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 1.341 Fit side-chains REVERT: B 186 ASP cc_start: 0.7485 (t0) cc_final: 0.7227 (t0) REVERT: B 259 LYS cc_start: 0.7380 (mtmt) cc_final: 0.6932 (ptpt) REVERT: E 259 LYS cc_start: 0.7384 (mtmt) cc_final: 0.6931 (ptpt) outliers start: 4 outliers final: 4 residues processed: 94 average time/residue: 0.2519 time to fit residues: 34.1061 Evaluate side-chains 87 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.0980 chunk 107 optimal weight: 0.0870 chunk 87 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 chunk 139 optimal weight: 0.7980 chunk 115 optimal weight: 0.0010 chunk 128 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 103 optimal weight: 0.4980 overall best weight: 0.2564 ------------------------------------------------------------------------------- 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: 0.8479 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11466 Z= 0.125 Angle : 0.436 7.293 15652 Z= 0.214 Chirality : 0.038 0.135 1754 Planarity : 0.005 0.037 2012 Dihedral : 3.735 20.040 1554 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.01 % Allowed : 5.78 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.22), residues: 1406 helix: 2.79 (0.22), residues: 506 sheet: 0.32 (0.40), residues: 178 loop : 0.86 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 511 HIS 0.003 0.001 HIS E 174 PHE 0.010 0.001 PHE B 265 TYR 0.009 0.001 TYR D 94 ARG 0.007 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 108 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 1.285 Fit side-chains REVERT: A 94 TYR cc_start: 0.8748 (OUTLIER) cc_final: 0.7677 (m-10) REVERT: B 259 LYS cc_start: 0.7374 (mtmt) cc_final: 0.6829 (ptpt) REVERT: E 259 LYS cc_start: 0.7368 (mtmt) cc_final: 0.6823 (ptpt) REVERT: D 94 TYR cc_start: 0.8766 (OUTLIER) cc_final: 0.7693 (m-10) outliers start: 12 outliers final: 4 residues processed: 104 average time/residue: 0.2849 time to fit residues: 41.4872 Evaluate side-chains 92 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 1.296 ------------------------------------------------------------------------------- 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 E residue 164 ILE 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: 4.9990 chunk 97 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 114 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.1132 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= 0.218 Angle : 0.474 4.394 15652 Z= 0.233 Chirality : 0.040 0.135 1754 Planarity : 0.005 0.035 2012 Dihedral : 3.823 20.013 1554 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.92 % Allowed : 6.62 % Favored : 92.46 % 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 (0.39), 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 0.005 0.001 HIS E 174 PHE 0.019 0.002 PHE E 121 TYR 0.012 0.001 TYR A 94 ARG 0.003 0.000 ARG D 106 *********************** 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 110 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 1.268 Fit side-chains REVERT: A 94 TYR cc_start: 0.8942 (OUTLIER) cc_final: 0.7880 (m-10) REVERT: B 259 LYS cc_start: 0.7454 (mtmt) cc_final: 0.6982 (ptpt) REVERT: E 259 LYS cc_start: 0.7457 (mtmt) cc_final: 0.6985 (ptpt) REVERT: D 94 TYR cc_start: 0.8959 (OUTLIER) cc_final: 0.7900 (m-10) outliers start: 11 outliers final: 8 residues processed: 108 average time/residue: 0.2536 time to fit residues: 39.0125 Evaluate side-chains 99 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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 226 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 520 ASP Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 520 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 77 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 11466 Z= 0.418 Angle : 0.562 5.478 15652 Z= 0.276 Chirality : 0.044 0.175 1754 Planarity : 0.005 0.033 2012 Dihedral : 4.163 20.136 1554 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.26 % Allowed : 6.95 % Favored : 91.79 % 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: 1.79 (0.22), residues: 1406 helix: 2.57 (0.22), residues: 506 sheet: -0.04 (0.38), residues: 178 loop : 0.63 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 168 HIS 0.007 0.001 HIS E 174 PHE 0.022 0.002 PHE E 121 TYR 0.016 0.002 TYR A 94 ARG 0.006 0.001 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 104 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 89 time to evaluate : 1.257 Fit side-chains REVERT: A 94 TYR cc_start: 0.9095 (OUTLIER) cc_final: 0.7736 (m-10) REVERT: B 186 ASP cc_start: 0.7486 (t0) cc_final: 0.7219 (t0) REVERT: B 259 LYS cc_start: 0.7516 (mtmt) cc_final: 0.7225 (ptpp) REVERT: E 259 LYS cc_start: 0.7515 (mtmt) cc_final: 0.7224 (ptpp) REVERT: D 94 TYR cc_start: 0.9108 (OUTLIER) cc_final: 0.7754 (m-10) outliers start: 15 outliers final: 8 residues processed: 101 average time/residue: 0.2497 time to fit residues: 36.3650 Evaluate side-chains 97 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 1.315 ------------------------------------------------------------------------------- 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 226 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 520 ASP 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 E residue 520 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: 0.9990 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 72 optimal weight: 0.0030 chunk 132 optimal weight: 1.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- 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: 0.8564 moved from start: 0.1413 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= 0.261 Angle : 0.491 4.737 15652 Z= 0.244 Chirality : 0.041 0.133 1754 Planarity : 0.005 0.034 2012 Dihedral : 4.018 20.241 1554 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.17 % Allowed : 8.04 % 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: 1.94 (0.22), residues: 1406 helix: 2.79 (0.22), residues: 506 sheet: -0.07 (0.38), residues: 178 loop : 0.66 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 214 HIS 0.005 0.001 HIS E 174 PHE 0.021 0.002 PHE E 121 TYR 0.012 0.001 TYR A 94 ARG 0.005 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 109 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 1.224 Fit side-chains REVERT: A 94 TYR cc_start: 0.9014 (OUTLIER) cc_final: 0.7726 (m-10) REVERT: B 186 ASP cc_start: 0.7512 (t0) cc_final: 0.7266 (t0) REVERT: B 259 LYS cc_start: 0.7484 (mtmt) cc_final: 0.7190 (ptpp) REVERT: E 259 LYS cc_start: 0.7491 (mtmt) cc_final: 0.7199 (ptpp) REVERT: D 94 TYR cc_start: 0.9038 (OUTLIER) cc_final: 0.7875 (m-10) outliers start: 14 outliers final: 10 residues processed: 105 average time/residue: 0.2385 time to fit residues: 36.5102 Evaluate side-chains 106 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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 B residue 520 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 E residue 520 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: 0.9980 chunk 78 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 77 optimal weight: 0.4980 chunk 115 optimal weight: 0.0970 chunk 76 optimal weight: 0.5980 chunk 136 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 63 optimal weight: 0.0060 chunk 84 optimal weight: 0.9980 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS D 146 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1435 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 : 0.451 4.603 15652 Z= 0.223 Chirality : 0.039 0.184 1754 Planarity : 0.004 0.034 2012 Dihedral : 3.788 20.057 1554 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.26 % Allowed : 8.04 % Favored : 90.70 % 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: 3.05 (0.22), residues: 506 sheet: -0.02 (0.38), residues: 178 loop : 0.77 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 214 HIS 0.004 0.001 HIS E 174 PHE 0.020 0.001 PHE E 121 TYR 0.009 0.001 TYR A 94 ARG 0.003 0.000 ARG A 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 116 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 1.236 Fit side-chains REVERT: A 94 TYR cc_start: 0.8954 (OUTLIER) cc_final: 0.7822 (m-10) REVERT: B 259 LYS cc_start: 0.7438 (mtmt) cc_final: 0.7144 (ptpp) REVERT: E 259 LYS cc_start: 0.7442 (mtmt) cc_final: 0.7152 (ptpp) REVERT: D 94 TYR cc_start: 0.8971 (OUTLIER) cc_final: 0.7847 (m-10) outliers start: 15 outliers final: 11 residues processed: 111 average time/residue: 0.2517 time to fit residues: 39.6244 Evaluate side-chains 109 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 226 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 520 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 E residue 520 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: 0.6980 chunk 81 optimal weight: 0.0270 chunk 41 optimal weight: 0.3980 chunk 26 optimal weight: 0.8980 chunk 87 optimal weight: 0.3980 chunk 93 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 107 optimal weight: 0.1980 chunk 124 optimal weight: 0.1980 chunk 131 optimal weight: 3.9990 overall best weight: 0.2438 ------------------------------------------------------------------------------- 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: 0.8501 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11466 Z= 0.130 Angle : 0.435 4.495 15652 Z= 0.214 Chirality : 0.038 0.134 1754 Planarity : 0.004 0.033 2012 Dihedral : 3.606 19.479 1554 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.17 % Allowed : 8.21 % 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: 2.37 (0.23), residues: 1406 helix: 3.21 (0.22), residues: 510 sheet: 0.08 (0.38), residues: 178 loop : 0.88 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 214 HIS 0.003 0.000 HIS E 174 PHE 0.018 0.001 PHE E 121 TYR 0.008 0.001 TYR A 94 ARG 0.003 0.000 ARG B 417 *********************** 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 118 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 1.300 Fit side-chains REVERT: A 94 TYR cc_start: 0.8802 (OUTLIER) cc_final: 0.7692 (m-10) REVERT: A 148 GLN cc_start: 0.8802 (pt0) cc_final: 0.8579 (pt0) REVERT: B 259 LYS cc_start: 0.7438 (mtmt) cc_final: 0.7186 (ptpp) REVERT: E 259 LYS cc_start: 0.7445 (mtmt) cc_final: 0.7192 (ptpp) REVERT: D 94 TYR cc_start: 0.8820 (OUTLIER) cc_final: 0.7857 (m-10) REVERT: D 148 GLN cc_start: 0.8805 (pt0) cc_final: 0.8576 (pt0) outliers start: 14 outliers final: 11 residues processed: 114 average time/residue: 0.2431 time to fit residues: 40.2009 Evaluate side-chains 113 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 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 A residue 354 GLU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 520 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 E residue 520 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: 0.0170 chunk 55 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 115 optimal weight: 0.4980 chunk 120 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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: 0.8525 moved from start: 0.1533 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= 0.188 Angle : 0.463 7.312 15652 Z= 0.226 Chirality : 0.040 0.193 1754 Planarity : 0.004 0.032 2012 Dihedral : 3.664 19.221 1554 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.01 % Allowed : 8.71 % 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: 2.35 (0.23), residues: 1406 helix: 3.21 (0.22), residues: 506 sheet: 0.09 (0.39), residues: 178 loop : 0.87 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 214 HIS 0.004 0.001 HIS E 174 PHE 0.018 0.001 PHE E 121 TYR 0.011 0.001 TYR A 94 ARG 0.003 0.000 ARG A 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 107 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 1.475 Fit side-chains REVERT: A 94 TYR cc_start: 0.8910 (OUTLIER) cc_final: 0.7724 (m-10) REVERT: B 259 LYS cc_start: 0.7448 (mtmt) cc_final: 0.7219 (ptpp) REVERT: E 259 LYS cc_start: 0.7461 (mtmt) cc_final: 0.7233 (ptpp) REVERT: D 94 TYR cc_start: 0.8931 (OUTLIER) cc_final: 0.7886 (m-10) outliers start: 12 outliers final: 10 residues processed: 104 average time/residue: 0.2376 time to fit residues: 35.7325 Evaluate side-chains 107 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 1.245 ------------------------------------------------------------------------------- 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 226 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 520 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 E residue 520 ASP Chi-restraints excluded: chain D residue 94 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 130 optimal weight: 0.0470 chunk 112 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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: 0.8540 moved from start: 0.1541 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= 0.206 Angle : 0.472 6.462 15652 Z= 0.232 Chirality : 0.040 0.166 1754 Planarity : 0.004 0.032 2012 Dihedral : 3.737 19.001 1554 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.01 % Allowed : 8.71 % 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: 2.28 (0.22), residues: 1406 helix: 3.14 (0.22), residues: 506 sheet: 0.09 (0.39), residues: 178 loop : 0.83 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 214 HIS 0.005 0.001 HIS E 174 PHE 0.018 0.002 PHE E 121 TYR 0.011 0.001 TYR A 94 ARG 0.003 0.000 ARG A 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 114 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 1.246 Fit side-chains REVERT: A 5 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8982 (mp) REVERT: A 94 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.7753 (m-10) REVERT: B 259 LYS cc_start: 0.7460 (mtmt) cc_final: 0.7246 (ptpp) REVERT: E 259 LYS cc_start: 0.7476 (mtmt) cc_final: 0.7264 (ptpp) REVERT: D 94 TYR cc_start: 0.9000 (OUTLIER) cc_final: 0.7899 (m-10) outliers start: 12 outliers final: 9 residues processed: 111 average time/residue: 0.2403 time to fit residues: 38.6476 Evaluate side-chains 108 residues out of total 1220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 B residue 164 ILE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 520 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 E residue 520 ASP Chi-restraints excluded: chain D residue 94 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.109785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.083895 restraints weight = 15564.574| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.21 r_work: 0.2767 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1592 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= 0.250 Angle : 0.508 13.169 15652 Z= 0.246 Chirality : 0.040 0.153 1754 Planarity : 0.005 0.032 2012 Dihedral : 3.843 19.006 1554 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.01 % Allowed : 8.71 % 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: 2.18 (0.22), residues: 1406 helix: 3.06 (0.22), residues: 506 sheet: 0.04 (0.39), residues: 178 loop : 0.76 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 168 HIS 0.005 0.001 HIS E 174 PHE 0.019 0.002 PHE E 121 TYR 0.013 0.001 TYR A 94 ARG 0.003 0.000 ARG D 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2281.34 seconds wall clock time: 41 minutes 33.84 seconds (2493.84 seconds total)