Starting phenix.real_space_refine on Sun Mar 10 23:45:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dxi_30910/03_2024/7dxi_30910.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dxi_30910/03_2024/7dxi_30910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dxi_30910/03_2024/7dxi_30910.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dxi_30910/03_2024/7dxi_30910.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dxi_30910/03_2024/7dxi_30910.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dxi_30910/03_2024/7dxi_30910.pdb" } resolution = 3.53 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= 0.000 sd= 0.002 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 Ca 2 9.91 5 S 24 5.16 5 C 3920 2.51 5 N 1064 2.21 5 O 1120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 108": "OE1" <-> "OE2" Residue "A ASP 147": "OD1" <-> "OD2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 348": "OD1" <-> "OD2" Residue "A TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 430": "OE1" <-> "OE2" Residue "A PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 446": "OD1" <-> "OD2" Residue "A TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A ASP 510": "OD1" <-> "OD2" Residue "A PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 555": "OE1" <-> "OE2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 586": "OE1" <-> "OE2" Residue "A GLU 593": "OE1" <-> "OE2" Residue "A ASP 594": "OD1" <-> "OD2" Residue "A TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B ASP 147": "OD1" <-> "OD2" Residue "B TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 348": "OD1" <-> "OD2" Residue "B TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 430": "OE1" <-> "OE2" Residue "B PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 446": "OD1" <-> "OD2" Residue "B TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 470": "OE1" <-> "OE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B ASP 510": "OD1" <-> "OD2" Residue "B PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 555": "OE1" <-> "OE2" Residue "B ASP 578": "OD1" <-> "OD2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B GLU 586": "OE1" <-> "OE2" Residue "B GLU 593": "OE1" <-> "OE2" Residue "B ASP 594": "OD1" <-> "OD2" Residue "B TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6130 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3064 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 20, 'TRANS': 350} Chain breaks: 3 Chain: "B" Number of atoms: 3064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3064 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 20, 'TRANS': 350} Chain breaks: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.93, per 1000 atoms: 0.64 Number of scatterers: 6130 At special positions: 0 Unit cell: (115.333, 115.333, 59.9472, 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) Ca 2 19.99 S 24 16.00 O 1120 8.00 N 1064 7.00 C 3920 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 515 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 515 " distance=2.03 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: 2.07 Conformation dependent library (CDL) restraints added in 1.1 seconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1452 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 8 sheets defined 45.8% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 75 through 85 removed outlier: 3.560A pdb=" N ILE A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASP A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 102 Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.727A pdb=" N LEU A 107 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 145 Processing helix chain 'A' and resid 155 through 160 removed outlier: 3.715A pdb=" N ILE A 159 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 166 removed outlier: 5.833A pdb=" N HIS A 164 " --> pdb=" O THR A 161 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG A 165 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE A 166 " --> pdb=" O LEU A 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 161 through 166' Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 349 through 364 removed outlier: 3.750A pdb=" N SER A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 390 Processing helix chain 'A' and resid 392 through 401 removed outlier: 3.592A pdb=" N LEU A 397 " --> pdb=" O HIS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 417 Processing helix chain 'A' and resid 428 through 435 Processing helix chain 'A' and resid 445 through 455 removed outlier: 3.561A pdb=" N ARG A 455 " --> pdb=" O THR A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 476 removed outlier: 3.615A pdb=" N MET A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS A 476 " --> pdb=" O VAL A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 515 removed outlier: 3.504A pdb=" N VAL A 512 " --> pdb=" O THR A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 524 Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.534A pdb=" N ARG A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN A 566 " --> pdb=" O ARG A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 600 removed outlier: 3.932A pdb=" N MET A 587 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG A 589 " --> pdb=" O ASN A 585 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A 599 " --> pdb=" O PHE A 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 85 removed outlier: 3.560A pdb=" N ILE B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASP B 81 " --> pdb=" O ASN B 77 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 102 Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.727A pdb=" N LEU B 107 " --> pdb=" O SER B 103 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 145 Processing helix chain 'B' and resid 155 through 160 removed outlier: 3.716A pdb=" N ILE B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 166 removed outlier: 5.833A pdb=" N HIS B 164 " --> pdb=" O THR B 161 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG B 165 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE B 166 " --> pdb=" O LEU B 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 161 through 166' Processing helix chain 'B' and resid 187 through 191 Processing helix chain 'B' and resid 349 through 364 removed outlier: 3.749A pdb=" N SER B 353 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA B 364 " --> pdb=" O LEU B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 390 Processing helix chain 'B' and resid 392 through 401 removed outlier: 3.592A pdb=" N LEU B 397 " --> pdb=" O HIS B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 417 Processing helix chain 'B' and resid 428 through 435 Processing helix chain 'B' and resid 445 through 455 removed outlier: 3.561A pdb=" N ARG B 455 " --> pdb=" O THR B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 476 removed outlier: 3.616A pdb=" N MET B 466 " --> pdb=" O ASP B 462 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS B 476 " --> pdb=" O VAL B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 515 removed outlier: 3.504A pdb=" N VAL B 512 " --> pdb=" O THR B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 524 Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.534A pdb=" N ARG B 564 " --> pdb=" O LEU B 560 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN B 566 " --> pdb=" O ARG B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 600 removed outlier: 3.932A pdb=" N MET B 587 " --> pdb=" O GLU B 583 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG B 589 " --> pdb=" O ASN B 585 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE B 599 " --> pdb=" O PHE B 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 68 removed outlier: 6.822A pdb=" N ALA A 66 " --> pdb=" O TYR A 118 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N VAL A 120 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TYR A 68 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 117 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL A 139 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE A 119 " --> pdb=" O VAL A 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 174 Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AA4, first strand: chain 'A' and resid 199 through 200 Processing sheet with id=AA5, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.822A pdb=" N ALA B 66 " --> pdb=" O TYR B 118 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N VAL B 120 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TYR B 68 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL B 117 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL B 139 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE B 119 " --> pdb=" O VAL B 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 172 through 174 Processing sheet with id=AA7, first strand: chain 'B' and resid 180 through 181 Processing sheet with id=AA8, first strand: chain 'B' and resid 199 through 200 168 hydrogen bonds defined for protein. 480 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: 1.40 Time building geometry restraints manager: 2.27 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: 1962 1.34 - 1.46: 1218 1.46 - 1.58: 3066 1.58 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 6286 Sorted by residual: bond pdb=" C GLN B 458 " pdb=" N PRO B 459 " ideal model delta sigma weight residual 1.329 1.351 -0.022 1.18e-02 7.18e+03 3.35e+00 bond pdb=" C GLN A 458 " pdb=" N PRO A 459 " ideal model delta sigma weight residual 1.329 1.350 -0.021 1.18e-02 7.18e+03 3.26e+00 bond pdb=" CA LYS A 368 " pdb=" C LYS A 368 " ideal model delta sigma weight residual 1.523 1.545 -0.021 1.34e-02 5.57e+03 2.55e+00 bond pdb=" CA LYS B 368 " pdb=" C LYS B 368 " ideal model delta sigma weight residual 1.523 1.544 -0.021 1.34e-02 5.57e+03 2.52e+00 bond pdb=" N LEU A 176 " pdb=" CA LEU A 176 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.31e-02 5.83e+03 2.34e+00 ... (remaining 6281 not shown) Histogram of bond angle deviations from ideal: 100.47 - 107.21: 272 107.21 - 113.94: 3304 113.94 - 120.67: 2764 120.67 - 127.41: 2116 127.41 - 134.14: 80 Bond angle restraints: 8536 Sorted by residual: angle pdb=" C PRO A 459 " pdb=" N PRO A 460 " pdb=" CD PRO A 460 " ideal model delta sigma weight residual 125.00 104.99 20.01 4.10e+00 5.95e-02 2.38e+01 angle pdb=" C PRO B 459 " pdb=" N PRO B 460 " pdb=" CD PRO B 460 " ideal model delta sigma weight residual 125.00 104.99 20.01 4.10e+00 5.95e-02 2.38e+01 angle pdb=" CA PRO A 460 " pdb=" N PRO A 460 " pdb=" CD PRO A 460 " ideal model delta sigma weight residual 112.00 105.33 6.67 1.40e+00 5.10e-01 2.27e+01 angle pdb=" CA PRO B 460 " pdb=" N PRO B 460 " pdb=" CD PRO B 460 " ideal model delta sigma weight residual 112.00 105.37 6.63 1.40e+00 5.10e-01 2.24e+01 angle pdb=" N LYS A 368 " pdb=" CA LYS A 368 " pdb=" C LYS A 368 " ideal model delta sigma weight residual 110.80 120.35 -9.55 2.13e+00 2.20e-01 2.01e+01 ... (remaining 8531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 3329 17.70 - 35.40: 365 35.40 - 53.11: 64 53.11 - 70.81: 12 70.81 - 88.51: 4 Dihedral angle restraints: 3774 sinusoidal: 1554 harmonic: 2220 Sorted by residual: dihedral pdb=" CA PHE A 367 " pdb=" C PHE A 367 " pdb=" N LYS A 368 " pdb=" CA LYS A 368 " ideal model delta harmonic sigma weight residual -180.00 -128.71 -51.29 0 5.00e+00 4.00e-02 1.05e+02 dihedral pdb=" CA PHE B 367 " pdb=" C PHE B 367 " pdb=" N LYS B 368 " pdb=" CA LYS B 368 " ideal model delta harmonic sigma weight residual -180.00 -128.74 -51.26 0 5.00e+00 4.00e-02 1.05e+02 dihedral pdb=" CB CYS A 476 " pdb=" SG CYS A 476 " pdb=" SG CYS A 515 " pdb=" CB CYS A 515 " ideal model delta sinusoidal sigma weight residual 93.00 -178.49 -88.51 1 1.00e+01 1.00e-02 9.35e+01 ... (remaining 3771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 629 0.053 - 0.105: 217 0.105 - 0.158: 63 0.158 - 0.211: 13 0.211 - 0.263: 10 Chirality restraints: 932 Sorted by residual: chirality pdb=" CA LYS A 368 " pdb=" N LYS A 368 " pdb=" C LYS A 368 " pdb=" CB LYS A 368 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA LYS B 368 " pdb=" N LYS B 368 " pdb=" C LYS B 368 " pdb=" CB LYS B 368 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA GLN B 458 " pdb=" N GLN B 458 " pdb=" C GLN B 458 " pdb=" CB GLN B 458 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 929 not shown) Planarity restraints: 1106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 459 " -0.130 5.00e-02 4.00e+02 1.98e-01 6.27e+01 pdb=" N PRO A 460 " 0.342 5.00e-02 4.00e+02 pdb=" CA PRO A 460 " -0.119 5.00e-02 4.00e+02 pdb=" CD PRO A 460 " -0.093 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 459 " 0.130 5.00e-02 4.00e+02 1.98e-01 6.25e+01 pdb=" N PRO B 460 " -0.341 5.00e-02 4.00e+02 pdb=" CA PRO B 460 " 0.119 5.00e-02 4.00e+02 pdb=" CD PRO B 460 " 0.093 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 151 " -0.076 5.00e-02 4.00e+02 1.16e-01 2.14e+01 pdb=" N PRO A 152 " 0.200 5.00e-02 4.00e+02 pdb=" CA PRO A 152 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 152 " -0.065 5.00e-02 4.00e+02 ... (remaining 1103 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.15: 2 2.15 - 2.84: 1965 2.84 - 3.53: 7955 3.53 - 4.21: 13695 4.21 - 4.90: 23490 Nonbonded interactions: 47107 Sorted by model distance: nonbonded pdb=" OD2 ASP B 439 " pdb=" OG1 THR B 443 " model vdw 1.468 2.440 nonbonded pdb=" OD2 ASP A 439 " pdb=" OG1 THR A 443 " model vdw 1.468 2.440 nonbonded pdb=" CB ASP A 439 " pdb="CA CA A 701 " model vdw 2.247 2.910 nonbonded pdb=" O THR B 443 " pdb="CA CA B 701 " model vdw 2.248 2.510 nonbonded pdb=" CB ASP B 439 " pdb="CA CA B 701 " model vdw 2.248 2.910 ... (remaining 47102 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 group one per residue 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: 2.400 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: 6.890 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 19.740 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 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 : 0.006 0.040 6286 Z= 0.401 Angle : 1.298 20.014 8536 Z= 0.676 Chirality : 0.064 0.263 932 Planarity : 0.012 0.198 1106 Dihedral : 15.064 76.380 2316 Min Nonbonded Distance : 1.468 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.55 % Allowed : 13.91 % Favored : 85.54 % Rotamer: Outliers : 0.30 % Allowed : 0.74 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 1.44 % 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: -5.04 (0.24), residues: 726 helix: -3.36 (0.19), residues: 304 sheet: -2.64 (0.75), residues: 36 loop : -3.47 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP A 463 HIS 0.014 0.002 HIS B 116 PHE 0.052 0.004 PHE B 436 TYR 0.064 0.004 TYR A 175 ARG 0.012 0.001 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 118 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.6946 (t0) REVERT: A 368 LYS cc_start: 0.6373 (pttp) cc_final: 0.6167 (pttp) REVERT: A 594 ASP cc_start: 0.8115 (t70) cc_final: 0.7628 (m-30) REVERT: B 149 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7037 (t0) REVERT: B 463 TRP cc_start: 0.6358 (p-90) cc_final: 0.6064 (p-90) REVERT: B 589 ARG cc_start: 0.7985 (mtm180) cc_final: 0.7755 (mtp180) outliers start: 2 outliers final: 0 residues processed: 118 average time/residue: 0.1874 time to fit residues: 28.9044 Evaluate side-chains 91 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain B residue 149 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS A 576 ASN B 116 HIS B 124 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6286 Z= 0.272 Angle : 0.777 12.342 8536 Z= 0.388 Chirality : 0.045 0.156 932 Planarity : 0.009 0.154 1106 Dihedral : 7.982 49.759 834 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.55 % Allowed : 15.29 % Favored : 84.16 % Rotamer: Outliers : 2.68 % Allowed : 7.74 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.29 % 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: -4.02 (0.28), residues: 726 helix: -2.18 (0.24), residues: 326 sheet: -2.17 (0.87), residues: 32 loop : -3.24 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 70 HIS 0.005 0.001 HIS A 116 PHE 0.017 0.002 PHE A 600 TYR 0.027 0.002 TYR B 412 ARG 0.004 0.000 ARG B 562 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 558 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6579 (pm20) REVERT: A 576 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.8299 (t0) REVERT: A 590 HIS cc_start: 0.7602 (m90) cc_final: 0.7384 (m90) REVERT: A 594 ASP cc_start: 0.8212 (t70) cc_final: 0.7919 (t0) REVERT: B 576 ASN cc_start: 0.8498 (t0) cc_final: 0.8041 (t0) REVERT: B 590 HIS cc_start: 0.7649 (m90) cc_final: 0.7400 (m90) REVERT: B 594 ASP cc_start: 0.8292 (t70) cc_final: 0.8050 (t0) outliers start: 18 outliers final: 12 residues processed: 116 average time/residue: 0.1727 time to fit residues: 26.7078 Evaluate side-chains 108 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 528 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 ASN B 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6286 Z= 0.274 Angle : 0.738 7.766 8536 Z= 0.376 Chirality : 0.046 0.178 932 Planarity : 0.007 0.102 1106 Dihedral : 7.730 53.098 834 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.55 % Allowed : 16.80 % Favored : 82.64 % Rotamer: Outliers : 2.53 % Allowed : 13.24 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.58 % 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: -3.56 (0.28), residues: 726 helix: -1.62 (0.26), residues: 326 sheet: -2.22 (0.84), residues: 32 loop : -3.15 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 70 HIS 0.003 0.001 HIS B 543 PHE 0.016 0.002 PHE B 600 TYR 0.027 0.002 TYR B 412 ARG 0.002 0.000 ARG A 562 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 107 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: A 558 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6671 (pm20) REVERT: A 590 HIS cc_start: 0.7538 (m90) cc_final: 0.7278 (m90) REVERT: A 594 ASP cc_start: 0.8181 (t70) cc_final: 0.7908 (t0) REVERT: B 576 ASN cc_start: 0.8511 (t0) cc_final: 0.8258 (t0) REVERT: B 590 HIS cc_start: 0.7549 (m90) cc_final: 0.7292 (m90) REVERT: B 594 ASP cc_start: 0.8236 (t70) cc_final: 0.7978 (t0) outliers start: 17 outliers final: 13 residues processed: 114 average time/residue: 0.1758 time to fit residues: 26.5757 Evaluate side-chains 111 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 526 PHE Chi-restraints excluded: chain B residue 528 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 71 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6286 Z= 0.197 Angle : 0.684 8.485 8536 Z= 0.348 Chirality : 0.043 0.166 932 Planarity : 0.006 0.099 1106 Dihedral : 7.177 52.492 834 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.19 % Favored : 85.81 % Rotamer: Outliers : 2.38 % Allowed : 17.71 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -3.24 (0.29), residues: 726 helix: -1.22 (0.27), residues: 332 sheet: -2.81 (0.69), residues: 42 loop : -3.06 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 70 HIS 0.003 0.001 HIS A 543 PHE 0.013 0.001 PHE A 419 TYR 0.021 0.002 TYR A 412 ARG 0.002 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 106 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: A 514 ARG cc_start: 0.5619 (ttt180) cc_final: 0.5395 (ptp-110) REVERT: A 547 MET cc_start: 0.6149 (mtt) cc_final: 0.5873 (mtt) REVERT: A 558 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6634 (pm20) REVERT: A 562 ARG cc_start: 0.8233 (ttp-170) cc_final: 0.7857 (ttp-170) REVERT: A 576 ASN cc_start: 0.8400 (OUTLIER) cc_final: 0.8107 (t0) REVERT: A 594 ASP cc_start: 0.8131 (t70) cc_final: 0.7926 (t0) REVERT: B 514 ARG cc_start: 0.5629 (ttt180) cc_final: 0.5376 (ptp-110) REVERT: B 576 ASN cc_start: 0.8413 (t0) cc_final: 0.7964 (t0) REVERT: B 590 HIS cc_start: 0.7514 (m90) cc_final: 0.7243 (m90) REVERT: B 594 ASP cc_start: 0.8112 (t70) cc_final: 0.7892 (t0) outliers start: 16 outliers final: 12 residues processed: 114 average time/residue: 0.1690 time to fit residues: 26.1292 Evaluate side-chains 111 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 526 PHE Chi-restraints excluded: chain B residue 563 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 61 optimal weight: 0.1980 chunk 49 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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: 0.8060 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6286 Z= 0.216 Angle : 0.684 8.074 8536 Z= 0.349 Chirality : 0.044 0.158 932 Planarity : 0.006 0.105 1106 Dihedral : 7.126 52.594 834 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.84 % Favored : 84.16 % Rotamer: Outliers : 3.42 % Allowed : 17.41 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -3.02 (0.30), residues: 726 helix: -1.07 (0.27), residues: 336 sheet: -2.61 (0.71), residues: 42 loop : -2.93 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 70 HIS 0.003 0.001 HIS B 543 PHE 0.012 0.001 PHE A 419 TYR 0.022 0.002 TYR B 412 ARG 0.002 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 547 MET cc_start: 0.6139 (mtt) cc_final: 0.5379 (mtt) REVERT: A 558 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6673 (pm20) REVERT: A 562 ARG cc_start: 0.8241 (ttp-170) cc_final: 0.7586 (ttp80) REVERT: B 423 GLU cc_start: 0.7728 (tp30) cc_final: 0.7450 (tp30) REVERT: B 547 MET cc_start: 0.6127 (mtt) cc_final: 0.5854 (mtt) REVERT: B 576 ASN cc_start: 0.8432 (t0) cc_final: 0.8196 (t0) REVERT: B 590 HIS cc_start: 0.7500 (m90) cc_final: 0.7221 (m90) REVERT: B 594 ASP cc_start: 0.8130 (t70) cc_final: 0.7909 (t0) outliers start: 23 outliers final: 15 residues processed: 112 average time/residue: 0.1589 time to fit residues: 24.5147 Evaluate side-chains 112 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 526 PHE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 563 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 59 optimal weight: 0.0020 chunk 33 optimal weight: 0.5980 chunk 5 optimal weight: 0.0970 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6286 Z= 0.171 Angle : 0.656 9.795 8536 Z= 0.336 Chirality : 0.043 0.160 932 Planarity : 0.006 0.105 1106 Dihedral : 6.206 32.907 830 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.09 % Favored : 86.91 % Rotamer: Outliers : 3.27 % Allowed : 17.86 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.66 (0.31), residues: 726 helix: -0.66 (0.28), residues: 330 sheet: -2.40 (0.74), residues: 42 loop : -2.84 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 70 HIS 0.003 0.001 HIS A 535 PHE 0.011 0.001 PHE B 595 TYR 0.019 0.001 TYR A 412 ARG 0.001 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 558 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6645 (pm20) REVERT: A 576 ASN cc_start: 0.8323 (OUTLIER) cc_final: 0.8013 (t0) REVERT: B 423 GLU cc_start: 0.7621 (tp30) cc_final: 0.7298 (tp30) REVERT: B 467 ARG cc_start: 0.8022 (mtt-85) cc_final: 0.7508 (tpp80) REVERT: B 547 MET cc_start: 0.6064 (mtt) cc_final: 0.5834 (mtt) REVERT: B 576 ASN cc_start: 0.8396 (t0) cc_final: 0.8138 (t0) REVERT: B 590 HIS cc_start: 0.7478 (m90) cc_final: 0.7213 (m90) outliers start: 22 outliers final: 13 residues processed: 129 average time/residue: 0.1417 time to fit residues: 25.5588 Evaluate side-chains 112 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 526 PHE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 553 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 0.0670 chunk 8 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 ASN B 411 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6286 Z= 0.209 Angle : 0.695 11.037 8536 Z= 0.352 Chirality : 0.043 0.149 932 Planarity : 0.006 0.109 1106 Dihedral : 6.277 33.553 830 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.15 % Favored : 84.85 % Rotamer: Outliers : 3.42 % Allowed : 20.24 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.65 (0.31), residues: 726 helix: -0.68 (0.28), residues: 336 sheet: -2.41 (0.73), residues: 42 loop : -2.84 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 444 HIS 0.003 0.001 HIS A 543 PHE 0.011 0.001 PHE A 419 TYR 0.020 0.002 TYR A 412 ARG 0.002 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 547 MET cc_start: 0.6109 (mtt) cc_final: 0.5764 (mtt) REVERT: A 558 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6618 (pm20) REVERT: A 562 ARG cc_start: 0.8317 (ttp-170) cc_final: 0.7962 (ttp-170) REVERT: A 576 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.8036 (t0) REVERT: B 423 GLU cc_start: 0.7579 (tp30) cc_final: 0.7300 (tp30) REVERT: B 467 ARG cc_start: 0.8032 (mtt-85) cc_final: 0.7538 (tpp80) REVERT: B 547 MET cc_start: 0.6089 (mtt) cc_final: 0.5870 (mtt) REVERT: B 590 HIS cc_start: 0.7456 (m90) cc_final: 0.7164 (m90) outliers start: 23 outliers final: 15 residues processed: 109 average time/residue: 0.1453 time to fit residues: 22.3570 Evaluate side-chains 112 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 526 PHE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 553 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 0.0570 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 ASN B 411 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6286 Z= 0.198 Angle : 0.693 11.307 8536 Z= 0.353 Chirality : 0.044 0.151 932 Planarity : 0.007 0.114 1106 Dihedral : 6.246 32.902 830 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.88 % Favored : 85.12 % Rotamer: Outliers : 2.98 % Allowed : 20.39 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.54 (0.31), residues: 726 helix: -0.55 (0.28), residues: 336 sheet: -2.60 (0.70), residues: 46 loop : -2.77 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 70 HIS 0.003 0.001 HIS A 543 PHE 0.011 0.001 PHE A 419 TYR 0.018 0.001 TYR A 412 ARG 0.001 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: A 547 MET cc_start: 0.6196 (mtt) cc_final: 0.5831 (mtt) REVERT: A 558 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6628 (pm20) REVERT: A 562 ARG cc_start: 0.8268 (ttp-170) cc_final: 0.7892 (ttp-170) REVERT: B 423 GLU cc_start: 0.7557 (tp30) cc_final: 0.7265 (tp30) REVERT: B 467 ARG cc_start: 0.8023 (mtt-85) cc_final: 0.7546 (tpp80) REVERT: B 547 MET cc_start: 0.6059 (mtt) cc_final: 0.5843 (mtt) REVERT: B 590 HIS cc_start: 0.7457 (m90) cc_final: 0.7180 (m90) outliers start: 20 outliers final: 15 residues processed: 105 average time/residue: 0.1501 time to fit residues: 21.8667 Evaluate side-chains 106 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 526 PHE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 553 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 52 optimal weight: 0.0000 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 70 optimal weight: 0.3980 chunk 42 optimal weight: 0.0010 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 411 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6286 Z= 0.176 Angle : 0.672 11.525 8536 Z= 0.343 Chirality : 0.043 0.152 932 Planarity : 0.007 0.116 1106 Dihedral : 6.001 30.899 830 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.60 % Favored : 85.40 % Rotamer: Outliers : 2.83 % Allowed : 20.54 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.30 (0.32), residues: 726 helix: -0.29 (0.29), residues: 330 sheet: -2.41 (0.73), residues: 46 loop : -2.69 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 70 HIS 0.002 0.001 HIS B 535 PHE 0.011 0.001 PHE A 595 TYR 0.016 0.001 TYR A 412 ARG 0.002 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 111 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: A 467 ARG cc_start: 0.8114 (mtt-85) cc_final: 0.7533 (tpp80) REVERT: A 558 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6606 (pm20) REVERT: B 467 ARG cc_start: 0.7990 (mtt-85) cc_final: 0.7548 (tpp80) REVERT: B 547 MET cc_start: 0.5988 (mtt) cc_final: 0.5757 (mtt) REVERT: B 590 HIS cc_start: 0.7438 (m90) cc_final: 0.7139 (m90) outliers start: 19 outliers final: 17 residues processed: 121 average time/residue: 0.1568 time to fit residues: 26.1769 Evaluate side-chains 119 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 526 PHE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 553 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 67 optimal weight: 0.1980 chunk 58 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN A 576 ASN B 411 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6286 Z= 0.213 Angle : 0.736 11.820 8536 Z= 0.367 Chirality : 0.044 0.154 932 Planarity : 0.007 0.119 1106 Dihedral : 6.121 31.395 830 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.01 % Favored : 84.99 % Rotamer: Outliers : 2.68 % Allowed : 22.02 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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 (0.31), residues: 726 helix: -0.30 (0.29), residues: 330 sheet: -2.54 (0.72), residues: 46 loop : -2.74 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 444 HIS 0.003 0.001 HIS A 371 PHE 0.010 0.001 PHE A 419 TYR 0.020 0.001 TYR A 412 ARG 0.002 0.000 ARG A 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: A 467 ARG cc_start: 0.8115 (mtt-85) cc_final: 0.7531 (tpp80) REVERT: A 558 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6554 (pm20) REVERT: B 467 ARG cc_start: 0.8004 (mtt-85) cc_final: 0.7533 (tpp80) REVERT: B 547 MET cc_start: 0.6019 (mtt) cc_final: 0.5808 (mtt) REVERT: B 590 HIS cc_start: 0.7451 (m90) cc_final: 0.7240 (m90) outliers start: 18 outliers final: 16 residues processed: 104 average time/residue: 0.1715 time to fit residues: 24.2830 Evaluate side-chains 108 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 411 GLN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 526 PHE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 553 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 0.4980 chunk 8 optimal weight: 0.0870 chunk 16 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN A 576 ASN B 411 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.142607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.118787 restraints weight = 9029.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.121713 restraints weight = 5727.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.123564 restraints weight = 4290.363| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6286 Z= 0.199 Angle : 0.731 11.924 8536 Z= 0.366 Chirality : 0.044 0.158 932 Planarity : 0.007 0.119 1106 Dihedral : 6.089 30.885 830 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.05 % Favored : 85.95 % Rotamer: Outliers : 2.83 % Allowed : 21.73 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.30 (0.31), residues: 726 helix: -0.26 (0.29), residues: 330 sheet: -2.52 (0.72), residues: 46 loop : -2.72 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 463 HIS 0.003 0.001 HIS A 371 PHE 0.010 0.001 PHE A 419 TYR 0.021 0.001 TYR A 412 ARG 0.007 0.000 ARG B 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1553.88 seconds wall clock time: 28 minutes 39.61 seconds (1719.61 seconds total)