Starting phenix.real_space_refine on Sat Apr 6 13:59:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tu9_41620/04_2024/8tu9_41620_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tu9_41620/04_2024/8tu9_41620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tu9_41620/04_2024/8tu9_41620.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tu9_41620/04_2024/8tu9_41620.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tu9_41620/04_2024/8tu9_41620_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tu9_41620/04_2024/8tu9_41620_updated.pdb" } resolution = 3.26 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= 0.006 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 38 5.16 5 C 5524 2.51 5 N 1348 2.21 5 O 1474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "B TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 607": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8390 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4102 Classifications: {'peptide': 533} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 26, 'TRANS': 506} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 68 Chain: "B" Number of atoms: 4102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4102 Classifications: {'peptide': 533} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 26, 'TRANS': 506} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 68 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 93 Unusual residues: {'ACO': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 93 Unusual residues: {'ACO': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.92, per 1000 atoms: 0.59 Number of scatterers: 8390 At special positions: 0 Unit cell: (77.35, 121.55, 105.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 6 15.00 O 1474 8.00 N 1348 7.00 C 5524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS A 79 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS B 334 " distance=2.05 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 434 " distance=2.02 Simple disulfide: pdb=" SG CYS B 76 " - pdb=" SG CYS B 79 " distance=2.03 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 434 " distance=2.02 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 Links applied NAG-ASN " NAG A 702 " - " ASN A 134 " " NAG A 703 " - " ASN A 433 " " NAG A 704 " - " ASN A 114 " " NAG B 702 " - " ASN B 134 " " NAG B 703 " - " ASN B 433 " " NAG B 704 " - " ASN B 114 " Time building additional restraints: 3.26 Conformation dependent library (CDL) restraints added in 1.7 seconds 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 4 sheets defined 46.0% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 164 through 181 Processing helix chain 'A' and resid 241 through 259 Processing helix chain 'A' and resid 278 through 301 removed outlier: 3.716A pdb=" N VAL A 281 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE A 282 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Proline residue: A 283 - end of helix removed outlier: 3.501A pdb=" N SER A 296 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR A 298 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 301 " --> pdb=" O THR A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 327 removed outlier: 3.989A pdb=" N GLY A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 326 " --> pdb=" O ILE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 365 Processing helix chain 'A' and resid 384 through 409 removed outlier: 4.003A pdb=" N SER A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TRP A 390 " --> pdb=" O ILE A 386 " (cutoff:3.500A) Proline residue: A 391 - end of helix removed outlier: 4.165A pdb=" N LEU A 394 " --> pdb=" O TRP A 390 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU A 395 " --> pdb=" O PRO A 391 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE A 396 " --> pdb=" O GLN A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 429 removed outlier: 3.672A pdb=" N GLY A 429 " --> pdb=" O GLY A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 426 through 429' Processing helix chain 'A' and resid 438 through 446 removed outlier: 3.523A pdb=" N ILE A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 446 " --> pdb=" O ILE A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 462 removed outlier: 3.949A pdb=" N VAL A 460 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 461 " --> pdb=" O SER A 458 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR A 462 " --> pdb=" O ALA A 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 457 through 462' Processing helix chain 'A' and resid 476 through 495 Processing helix chain 'A' and resid 500 through 522 Processing helix chain 'A' and resid 540 through 558 removed outlier: 3.744A pdb=" N SER A 548 " --> pdb=" O THR A 544 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 549 " --> pdb=" O THR A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 577 No H-bonds generated for 'chain 'A' and resid 574 through 577' Processing helix chain 'A' and resid 580 through 588 Processing helix chain 'A' and resid 605 through 629 removed outlier: 4.008A pdb=" N THR A 610 " --> pdb=" O LYS A 606 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLN A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 181 Processing helix chain 'B' and resid 241 through 259 Processing helix chain 'B' and resid 278 through 301 removed outlier: 3.715A pdb=" N VAL B 281 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE B 282 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Proline residue: B 283 - end of helix removed outlier: 3.501A pdb=" N SER B 296 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR B 298 " --> pdb=" O LEU B 295 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU B 301 " --> pdb=" O THR B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 327 removed outlier: 3.989A pdb=" N GLY B 312 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS B 313 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B 326 " --> pdb=" O ILE B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 365 Processing helix chain 'B' and resid 384 through 409 removed outlier: 4.003A pdb=" N SER B 389 " --> pdb=" O ASP B 385 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TRP B 390 " --> pdb=" O ILE B 386 " (cutoff:3.500A) Proline residue: B 391 - end of helix removed outlier: 4.165A pdb=" N LEU B 394 " --> pdb=" O TRP B 390 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU B 395 " --> pdb=" O PRO B 391 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE B 396 " --> pdb=" O GLN B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 429 removed outlier: 3.672A pdb=" N GLY B 429 " --> pdb=" O GLY B 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 426 through 429' Processing helix chain 'B' and resid 438 through 446 removed outlier: 3.524A pdb=" N ILE B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 446 " --> pdb=" O ILE B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 462 removed outlier: 3.948A pdb=" N VAL B 460 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 461 " --> pdb=" O SER B 458 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR B 462 " --> pdb=" O ALA B 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 457 through 462' Processing helix chain 'B' and resid 476 through 495 Processing helix chain 'B' and resid 500 through 522 Processing helix chain 'B' and resid 540 through 558 removed outlier: 3.745A pdb=" N SER B 548 " --> pdb=" O THR B 544 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE B 549 " --> pdb=" O THR B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 577 No H-bonds generated for 'chain 'B' and resid 574 through 577' Processing helix chain 'B' and resid 580 through 588 Processing helix chain 'B' and resid 605 through 629 removed outlier: 4.008A pdb=" N THR B 610 " --> pdb=" O LYS B 606 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLN B 611 " --> pdb=" O GLU B 607 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 97 through 104 removed outlier: 6.440A pdb=" N TYR A 135 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N HIS A 59 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU A 137 " --> pdb=" O HIS A 59 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 150 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU A 148 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 123 through 127 removed outlier: 3.890A pdb=" N CYS A 123 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A 85 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N TRP A 71 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL A 83 " --> pdb=" O TRP A 71 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 97 through 104 removed outlier: 6.440A pdb=" N TYR B 135 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N HIS B 59 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU B 137 " --> pdb=" O HIS B 59 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 150 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU B 148 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 123 through 127 removed outlier: 3.889A pdb=" N CYS B 123 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B 85 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N TRP B 71 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL B 83 " --> pdb=" O TRP B 71 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 1002 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: 1.96 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 2 1.13 - 1.31: 1266 1.31 - 1.49: 3704 1.49 - 1.66: 3602 1.66 - 1.84: 52 Bond restraints: 8626 Sorted by residual: bond pdb=" CB PRO A 371 " pdb=" CG PRO A 371 " ideal model delta sigma weight residual 1.492 0.953 0.539 5.00e-02 4.00e+02 1.16e+02 bond pdb=" CB PRO B 371 " pdb=" CG PRO B 371 " ideal model delta sigma weight residual 1.492 0.953 0.539 5.00e-02 4.00e+02 1.16e+02 bond pdb=" CG PRO A 371 " pdb=" CD PRO A 371 " ideal model delta sigma weight residual 1.503 1.232 0.271 3.40e-02 8.65e+02 6.34e+01 bond pdb=" CG PRO B 371 " pdb=" CD PRO B 371 " ideal model delta sigma weight residual 1.503 1.233 0.270 3.40e-02 8.65e+02 6.33e+01 bond pdb=" C1 NAG A 703 " pdb=" O5 NAG A 703 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 9.11e+00 ... (remaining 8621 not shown) Histogram of bond angle deviations from ideal: 75.99 - 96.78: 4 96.78 - 117.57: 6414 117.57 - 138.37: 5378 138.37 - 159.16: 0 159.16 - 179.95: 2 Bond angle restraints: 11798 Sorted by residual: angle pdb=" CB PRO A 371 " pdb=" CG PRO A 371 " pdb=" CD PRO A 371 " ideal model delta sigma weight residual 106.10 179.95 -73.85 3.20e+00 9.77e-02 5.33e+02 angle pdb=" CB PRO B 371 " pdb=" CG PRO B 371 " pdb=" CD PRO B 371 " ideal model delta sigma weight residual 106.10 179.93 -73.83 3.20e+00 9.77e-02 5.32e+02 angle pdb=" N PRO B 371 " pdb=" CD PRO B 371 " pdb=" CG PRO B 371 " ideal model delta sigma weight residual 103.20 77.97 25.23 1.50e+00 4.44e-01 2.83e+02 angle pdb=" N PRO A 371 " pdb=" CD PRO A 371 " pdb=" CG PRO A 371 " ideal model delta sigma weight residual 103.20 77.99 25.21 1.50e+00 4.44e-01 2.82e+02 angle pdb=" CA PRO A 371 " pdb=" CB PRO A 371 " pdb=" CG PRO A 371 " ideal model delta sigma weight residual 104.50 75.99 28.51 1.90e+00 2.77e-01 2.25e+02 ... (remaining 11793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 4539 17.01 - 34.02: 430 34.02 - 51.02: 84 51.02 - 68.03: 26 68.03 - 85.04: 8 Dihedral angle restraints: 5087 sinusoidal: 2009 harmonic: 3078 Sorted by residual: dihedral pdb=" CA LYS A 600 " pdb=" C LYS A 600 " pdb=" N ASP A 601 " pdb=" CA ASP A 601 " ideal model delta harmonic sigma weight residual 180.00 158.53 21.47 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA LYS B 600 " pdb=" C LYS B 600 " pdb=" N ASP B 601 " pdb=" CA ASP B 601 " ideal model delta harmonic sigma weight residual 180.00 158.54 21.46 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA LYS B 564 " pdb=" C LYS B 564 " pdb=" N GLY B 565 " pdb=" CA GLY B 565 " ideal model delta harmonic sigma weight residual -180.00 -158.77 -21.23 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 5084 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 1300 0.144 - 0.289: 60 0.289 - 0.433: 6 0.433 - 0.577: 2 0.577 - 0.721: 2 Chirality restraints: 1370 Sorted by residual: chirality pdb=" C1 NAG B 704 " pdb=" ND2 ASN B 114 " pdb=" C2 NAG B 704 " pdb=" O5 NAG B 704 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" C1 NAG A 704 " pdb=" ND2 ASN A 114 " pdb=" C2 NAG A 704 " pdb=" O5 NAG A 704 " both_signs ideal model delta sigma weight residual False -2.40 -1.68 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" C1 NAG B 703 " pdb=" ND2 ASN B 433 " pdb=" C2 NAG B 703 " pdb=" O5 NAG B 703 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.29e+00 ... (remaining 1367 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 531 " -0.111 5.00e-02 4.00e+02 1.65e-01 4.37e+01 pdb=" N PRO B 532 " 0.286 5.00e-02 4.00e+02 pdb=" CA PRO B 532 " -0.093 5.00e-02 4.00e+02 pdb=" CD PRO B 532 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 531 " 0.111 5.00e-02 4.00e+02 1.65e-01 4.36e+01 pdb=" N PRO A 532 " -0.286 5.00e-02 4.00e+02 pdb=" CA PRO A 532 " 0.093 5.00e-02 4.00e+02 pdb=" CD PRO A 532 " 0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 506 " -0.519 9.50e-02 1.11e+02 2.33e-01 3.63e+01 pdb=" NE ARG A 506 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG A 506 " -0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG A 506 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 506 " -0.007 2.00e-02 2.50e+03 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1922 2.80 - 3.32: 7350 3.32 - 3.85: 12795 3.85 - 4.37: 13822 4.37 - 4.90: 25745 Nonbonded interactions: 61634 Sorted by model distance: nonbonded pdb=" OG1 THR A 568 " pdb=" OG1 THR A 570 " model vdw 2.275 2.440 nonbonded pdb=" OG1 THR B 568 " pdb=" OG1 THR B 570 " model vdw 2.275 2.440 nonbonded pdb=" O PRO B 88 " pdb=" OG SER B 97 " model vdw 2.414 2.440 nonbonded pdb=" O PRO A 88 " pdb=" OG SER A 97 " model vdw 2.415 2.440 nonbonded pdb=" O LEU B 540 " pdb=" OG1 THR B 544 " model vdw 2.420 2.440 ... (remaining 61629 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.940 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.220 Find NCS groups from input model: 0.420 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 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 : 0.011 0.539 8626 Z= 0.676 Angle : 1.677 73.855 11798 Z= 0.825 Chirality : 0.078 0.721 1370 Planarity : 0.017 0.233 1434 Dihedral : 14.551 85.038 3104 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: -0.68 (0.24), residues: 1058 helix: 1.05 (0.21), residues: 482 sheet: 0.88 (0.53), residues: 114 loop : -2.58 (0.24), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 403 HIS 0.016 0.004 HIS A 586 PHE 0.043 0.003 PHE B 246 TYR 0.052 0.003 TYR A 127 ARG 0.030 0.005 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.908 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1562 time to fit residues: 15.7956 Evaluate side-chains 50 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 54 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 258 ASN B 59 HIS B 258 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8626 Z= 0.216 Angle : 0.627 7.957 11798 Z= 0.334 Chirality : 0.046 0.277 1370 Planarity : 0.007 0.091 1434 Dihedral : 10.375 86.590 1368 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.83 % Allowed : 4.48 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.25), residues: 1058 helix: 1.84 (0.23), residues: 480 sheet: 0.47 (0.45), residues: 128 loop : -2.20 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 403 HIS 0.006 0.001 HIS B 608 PHE 0.028 0.002 PHE A 246 TYR 0.025 0.002 TYR B 453 ARG 0.003 0.001 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.881 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 63 average time/residue: 0.1553 time to fit residues: 15.3715 Evaluate side-chains 56 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 104 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 HIS ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 8626 Z= 0.536 Angle : 0.811 7.152 11798 Z= 0.433 Chirality : 0.054 0.328 1370 Planarity : 0.007 0.066 1434 Dihedral : 9.742 64.339 1368 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.77 % Allowed : 7.67 % Favored : 90.57 % 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: -0.58 (0.24), residues: 1058 helix: 1.06 (0.23), residues: 468 sheet: 0.76 (0.45), residues: 126 loop : -2.34 (0.24), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 340 HIS 0.006 0.003 HIS A 608 PHE 0.036 0.003 PHE A 246 TYR 0.036 0.003 TYR A 453 ARG 0.004 0.001 ARG B 344 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 70 time to evaluate : 0.875 Fit side-chains REVERT: B 581 LEU cc_start: 0.8121 (mt) cc_final: 0.7898 (tt) outliers start: 15 outliers final: 11 residues processed: 79 average time/residue: 0.2029 time to fit residues: 22.9342 Evaluate side-chains 71 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 60 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 390 TRP Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain B residue 75 CYS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 390 TRP Chi-restraints excluded: chain B residue 533 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 586 HIS A 605 HIS B 59 HIS B 586 HIS B 605 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8626 Z= 0.174 Angle : 0.557 7.257 11798 Z= 0.293 Chirality : 0.044 0.232 1370 Planarity : 0.005 0.043 1434 Dihedral : 8.869 59.220 1368 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.18 % Allowed : 11.08 % Favored : 87.74 % 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: 0.23 (0.25), residues: 1058 helix: 1.94 (0.24), residues: 468 sheet: 1.24 (0.45), residues: 124 loop : -2.19 (0.24), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 390 HIS 0.003 0.001 HIS A 608 PHE 0.016 0.001 PHE A 573 TYR 0.018 0.001 TYR B 542 ARG 0.002 0.000 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.882 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 65 average time/residue: 0.1477 time to fit residues: 15.5736 Evaluate side-chains 58 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 390 TRP Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 390 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 76 optimal weight: 0.0570 chunk 42 optimal weight: 5.9990 chunk 87 optimal weight: 0.0970 chunk 70 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 0.0470 chunk 91 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS B 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8626 Z= 0.144 Angle : 0.501 6.855 11798 Z= 0.261 Chirality : 0.042 0.216 1370 Planarity : 0.004 0.035 1434 Dihedral : 8.126 54.907 1368 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.65 % Allowed : 12.26 % Favored : 86.08 % 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: 0.62 (0.26), residues: 1058 helix: 2.24 (0.24), residues: 478 sheet: 1.51 (0.47), residues: 116 loop : -2.02 (0.24), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 390 HIS 0.003 0.001 HIS A 608 PHE 0.012 0.001 PHE B 573 TYR 0.015 0.001 TYR A 542 ARG 0.002 0.000 ARG B 506 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 0.946 Fit side-chains outliers start: 14 outliers final: 14 residues processed: 65 average time/residue: 0.1346 time to fit residues: 14.8094 Evaluate side-chains 61 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 47 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 390 TRP Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 390 TRP Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 568 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 98 optimal weight: 0.0370 overall best weight: 2.1264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 332 ASN ** A 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 HIS B 332 ASN ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8626 Z= 0.334 Angle : 0.630 6.100 11798 Z= 0.335 Chirality : 0.047 0.254 1370 Planarity : 0.005 0.037 1434 Dihedral : 8.456 53.691 1368 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.30 % Allowed : 11.08 % Favored : 85.61 % 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: 0.15 (0.25), residues: 1058 helix: 1.73 (0.23), residues: 476 sheet: 1.53 (0.49), residues: 116 loop : -2.17 (0.24), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 403 HIS 0.005 0.001 HIS B 608 PHE 0.020 0.002 PHE B 573 TYR 0.019 0.002 TYR A 542 ARG 0.002 0.001 ARG A 351 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 53 time to evaluate : 0.984 Fit side-chains outliers start: 28 outliers final: 20 residues processed: 72 average time/residue: 0.1438 time to fit residues: 16.5652 Evaluate side-chains 72 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 52 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 390 TRP Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 390 TRP Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 568 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 612 ASN B 59 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8626 Z= 0.205 Angle : 0.544 6.296 11798 Z= 0.287 Chirality : 0.043 0.235 1370 Planarity : 0.004 0.035 1434 Dihedral : 8.239 52.073 1368 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.71 % Allowed : 12.03 % Favored : 85.26 % 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: 0.38 (0.26), residues: 1058 helix: 1.97 (0.24), residues: 476 sheet: 1.61 (0.49), residues: 116 loop : -2.10 (0.24), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 390 HIS 0.004 0.001 HIS B 608 PHE 0.015 0.001 PHE A 573 TYR 0.018 0.001 TYR A 542 ARG 0.002 0.000 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 50 time to evaluate : 0.847 Fit side-chains outliers start: 23 outliers final: 18 residues processed: 69 average time/residue: 0.1527 time to fit residues: 16.9502 Evaluate side-chains 66 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 48 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 390 TRP Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 390 TRP Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 533 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS B 59 HIS ** B 612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 8626 Z= 0.369 Angle : 0.644 5.949 11798 Z= 0.342 Chirality : 0.047 0.264 1370 Planarity : 0.005 0.038 1434 Dihedral : 8.539 55.466 1368 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.18 % Allowed : 12.26 % Favored : 84.55 % 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: 0.03 (0.25), residues: 1058 helix: 1.62 (0.23), residues: 468 sheet: 1.18 (0.47), residues: 130 loop : -2.17 (0.25), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 403 HIS 0.006 0.002 HIS B 608 PHE 0.020 0.002 PHE A 573 TYR 0.020 0.002 TYR B 453 ARG 0.002 0.001 ARG B 444 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 53 time to evaluate : 0.934 Fit side-chains REVERT: A 564 LYS cc_start: 0.8206 (ptpt) cc_final: 0.8006 (ptpp) outliers start: 27 outliers final: 21 residues processed: 71 average time/residue: 0.1431 time to fit residues: 16.4814 Evaluate side-chains 70 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 49 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 390 TRP Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 86 ASN Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 390 TRP Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 533 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 62 optimal weight: 20.0000 chunk 100 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 612 ASN B 59 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8626 Z= 0.173 Angle : 0.518 6.054 11798 Z= 0.273 Chirality : 0.042 0.226 1370 Planarity : 0.004 0.034 1434 Dihedral : 8.174 53.762 1368 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.89 % Allowed : 13.68 % Favored : 84.43 % 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: 0.58 (0.26), residues: 1058 helix: 2.18 (0.24), residues: 468 sheet: 1.74 (0.50), residues: 112 loop : -1.95 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 390 HIS 0.004 0.001 HIS B 586 PHE 0.013 0.001 PHE A 573 TYR 0.017 0.001 TYR A 542 ARG 0.002 0.000 ARG B 444 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 47 time to evaluate : 0.836 Fit side-chains REVERT: A 564 LYS cc_start: 0.8138 (ptpt) cc_final: 0.7937 (ptpp) outliers start: 16 outliers final: 14 residues processed: 61 average time/residue: 0.1390 time to fit residues: 14.0958 Evaluate side-chains 61 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 47 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 533 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 612 ASN B 59 HIS B 612 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8626 Z= 0.262 Angle : 0.574 5.881 11798 Z= 0.303 Chirality : 0.045 0.243 1370 Planarity : 0.004 0.033 1434 Dihedral : 8.248 54.265 1368 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.89 % Allowed : 13.68 % Favored : 84.43 % 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: 0.33 (0.26), residues: 1058 helix: 1.91 (0.24), residues: 474 sheet: 1.55 (0.48), residues: 116 loop : -2.08 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 390 HIS 0.006 0.001 HIS B 586 PHE 0.016 0.001 PHE A 573 TYR 0.018 0.001 TYR A 542 ARG 0.002 0.000 ARG A 351 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 47 time to evaluate : 0.870 Fit side-chains REVERT: A 389 SER cc_start: 0.8070 (OUTLIER) cc_final: 0.7778 (p) REVERT: A 564 LYS cc_start: 0.8166 (ptpt) cc_final: 0.7965 (ptpp) REVERT: B 389 SER cc_start: 0.8066 (OUTLIER) cc_final: 0.7774 (p) outliers start: 16 outliers final: 14 residues processed: 61 average time/residue: 0.1432 time to fit residues: 14.4668 Evaluate side-chains 63 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 47 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 389 SER Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 533 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 23 optimal weight: 0.0670 chunk 84 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 4 optimal weight: 9.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 612 ASN B 59 HIS B 612 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.163926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.132474 restraints weight = 10396.208| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.93 r_work: 0.3466 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8626 Z= 0.175 Angle : 0.516 5.976 11798 Z= 0.271 Chirality : 0.042 0.225 1370 Planarity : 0.004 0.031 1434 Dihedral : 8.059 55.232 1368 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.77 % Allowed : 13.56 % Favored : 84.67 % 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: 0.60 (0.26), residues: 1058 helix: 2.17 (0.24), residues: 474 sheet: 1.76 (0.49), residues: 112 loop : -1.96 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 265 HIS 0.004 0.001 HIS B 586 PHE 0.013 0.001 PHE A 573 TYR 0.017 0.001 TYR A 542 ARG 0.001 0.000 ARG A 444 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1696.85 seconds wall clock time: 31 minutes 57.29 seconds (1917.29 seconds total)