Starting phenix.real_space_refine on Wed May 8 05:00:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur3_42480/05_2024/8ur3_42480.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur3_42480/05_2024/8ur3_42480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur3_42480/05_2024/8ur3_42480.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur3_42480/05_2024/8ur3_42480.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur3_42480/05_2024/8ur3_42480.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ur3_42480/05_2024/8ur3_42480.pdb" } resolution = 2.61 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 5982 2.51 5 N 1544 2.21 5 O 1806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 9376 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4688 Classifications: {'peptide': 579} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 555} Chain breaks: 1 Chain: "B" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4688 Classifications: {'peptide': 579} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 555} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N ARG A 78 " occ=0.86 ... (9 atoms not shown) pdb=" NH2 ARG A 78 " occ=0.86 residue: pdb=" N GLY A 79 " occ=0.82 ... (2 atoms not shown) pdb=" O GLY A 79 " occ=0.82 residue: pdb=" N GLY A 80 " occ=0.83 ... (2 atoms not shown) pdb=" O GLY A 80 " occ=0.83 residue: pdb=" N ARG A 81 " occ=0.62 ... (9 atoms not shown) pdb=" NH2 ARG A 81 " occ=0.62 residue: pdb=" N ARG B 78 " occ=0.86 ... (9 atoms not shown) pdb=" NH2 ARG B 78 " occ=0.86 residue: pdb=" N GLY B 79 " occ=0.82 ... (2 atoms not shown) pdb=" O GLY B 79 " occ=0.82 residue: pdb=" N GLY B 80 " occ=0.83 ... (2 atoms not shown) pdb=" O GLY B 80 " occ=0.83 residue: pdb=" N ARG B 81 " occ=0.62 ... (9 atoms not shown) pdb=" NH2 ARG B 81 " occ=0.62 Time building chain proxies: 5.51, per 1000 atoms: 0.59 Number of scatterers: 9376 At special positions: 0 Unit cell: (101.268, 115.884, 82.476, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1806 8.00 N 1544 7.00 C 5982 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.7 seconds 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2204 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 8 sheets defined 42.7% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 6 through 12 removed outlier: 3.536A pdb=" N ALA A 10 " --> pdb=" O GLY A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 23 removed outlier: 3.519A pdb=" N ASN A 22 " --> pdb=" O ASN A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 44 Processing helix chain 'A' and resid 48 through 50 No H-bonds generated for 'chain 'A' and resid 48 through 50' Processing helix chain 'A' and resid 87 through 94 Processing helix chain 'A' and resid 106 through 118 Processing helix chain 'A' and resid 143 through 155 Processing helix chain 'A' and resid 158 through 162 removed outlier: 3.991A pdb=" N ASP A 162 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.596A pdb=" N PHE A 175 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 187 removed outlier: 3.571A pdb=" N ILE A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 185 " --> pdb=" O ILE A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'A' and resid 206 through 209 removed outlier: 3.771A pdb=" N ILE A 209 " --> pdb=" O VAL A 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 206 through 209' Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 229 through 240 removed outlier: 3.533A pdb=" N HIS A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 324 Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.670A pdb=" N GLY A 330 " --> pdb=" O PRO A 327 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ASN A 331 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 354 through 366 Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 431 through 443 Processing helix chain 'A' and resid 449 through 456 removed outlier: 3.643A pdb=" N LEU A 453 " --> pdb=" O LYS A 449 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 454 " --> pdb=" O ILE A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 523 removed outlier: 3.584A pdb=" N SER A 511 " --> pdb=" O THR A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 537 Processing helix chain 'A' and resid 538 through 550 removed outlier: 3.682A pdb=" N ASN A 550 " --> pdb=" O ILE A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 559 Processing helix chain 'A' and resid 562 through 576 Processing helix chain 'A' and resid 579 through 588 Processing helix chain 'B' and resid 6 through 12 removed outlier: 3.536A pdb=" N ALA B 10 " --> pdb=" O GLY B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.521A pdb=" N ASN B 22 " --> pdb=" O ASN B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 44 Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 106 through 118 Processing helix chain 'B' and resid 143 through 155 Processing helix chain 'B' and resid 158 through 162 removed outlier: 3.988A pdb=" N ASP B 162 " --> pdb=" O GLU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.593A pdb=" N PHE B 175 " --> pdb=" O SER B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 187 removed outlier: 3.571A pdb=" N ILE B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B 185 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 206 through 209 removed outlier: 3.771A pdb=" N ILE B 209 " --> pdb=" O VAL B 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 206 through 209' Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 229 through 240 removed outlier: 3.525A pdb=" N HIS B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 324 Processing helix chain 'B' and resid 326 through 331 removed outlier: 3.663A pdb=" N GLY B 330 " --> pdb=" O PRO B 327 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ASN B 331 " --> pdb=" O GLU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 354 through 366 Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 431 through 443 Processing helix chain 'B' and resid 449 through 456 removed outlier: 3.640A pdb=" N LEU B 453 " --> pdb=" O LYS B 449 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 523 removed outlier: 3.584A pdb=" N SER B 511 " --> pdb=" O THR B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 537 Processing helix chain 'B' and resid 538 through 550 removed outlier: 3.681A pdb=" N ASN B 550 " --> pdb=" O ILE B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 559 Processing helix chain 'B' and resid 562 through 576 Processing helix chain 'B' and resid 579 through 588 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'A' and resid 243 through 245 removed outlier: 6.273A pdb=" N ILE A 52 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLU A 245 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ILE A 54 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA A 25 " --> pdb=" O HIS A 53 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N LEU A 55 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU A 27 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR A 289 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL A 286 " --> pdb=" O ALA A 492 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILE A 494 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL A 288 " --> pdb=" O ILE A 494 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 133 removed outlier: 4.384A pdb=" N MET A 389 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA A 413 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N VAL A 346 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 248 through 257 removed outlier: 6.032A pdb=" N VAL A 250 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASP A 270 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP A 252 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A 266 " --> pdb=" O LYS A 254 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ASP A 256 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA A 264 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 4 Processing sheet with id=AA6, first strand: chain 'B' and resid 243 through 245 removed outlier: 6.268A pdb=" N ILE B 52 " --> pdb=" O GLN B 243 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLU B 245 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ILE B 54 " --> pdb=" O GLU B 245 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA B 25 " --> pdb=" O HIS B 53 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU B 55 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU B 27 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR B 289 " --> pdb=" O ILE B 28 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ALA B 492 " --> pdb=" O ASP B 284 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL B 286 " --> pdb=" O ALA B 492 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE B 494 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL B 288 " --> pdb=" O ILE B 494 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 132 through 133 removed outlier: 4.385A pdb=" N MET B 389 " --> pdb=" O ILE B 382 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA B 413 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N VAL B 346 " --> pdb=" O ALA B 413 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 248 through 257 removed outlier: 6.037A pdb=" N VAL B 250 " --> pdb=" O ASP B 270 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASP B 270 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP B 252 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU B 266 " --> pdb=" O LYS B 254 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASP B 256 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA B 264 " --> pdb=" O ASP B 256 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 951 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: 2.93 Time building geometry restraints manager: 3.64 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: 3033 1.34 - 1.46: 1785 1.46 - 1.57: 4702 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 9592 Sorted by residual: bond pdb=" C ILE A 581 " pdb=" O ILE A 581 " ideal model delta sigma weight residual 1.237 1.225 0.013 1.17e-02 7.31e+03 1.15e+00 bond pdb=" N ILE A 461 " pdb=" CA ILE A 461 " ideal model delta sigma weight residual 1.458 1.450 0.008 7.70e-03 1.69e+04 1.02e+00 bond pdb=" CB GLU A 110 " pdb=" CG GLU A 110 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.82e-01 bond pdb=" CA ILE A 461 " pdb=" C ILE A 461 " ideal model delta sigma weight residual 1.528 1.536 -0.008 8.50e-03 1.38e+04 9.33e-01 bond pdb=" CB GLU B 110 " pdb=" CG GLU B 110 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.23e-01 ... (remaining 9587 not shown) Histogram of bond angle deviations from ideal: 99.60 - 106.51: 242 106.51 - 113.42: 5214 113.42 - 120.33: 3494 120.33 - 127.24: 3934 127.24 - 134.15: 114 Bond angle restraints: 12998 Sorted by residual: angle pdb=" C HIS A 588 " pdb=" N LYS A 589 " pdb=" CA LYS A 589 " ideal model delta sigma weight residual 121.54 127.31 -5.77 1.91e+00 2.74e-01 9.14e+00 angle pdb=" C HIS B 588 " pdb=" N LYS B 589 " pdb=" CA LYS B 589 " ideal model delta sigma weight residual 121.54 127.29 -5.75 1.91e+00 2.74e-01 9.07e+00 angle pdb=" C GLN A 396 " pdb=" N GLN A 397 " pdb=" CA GLN A 397 " ideal model delta sigma weight residual 121.70 126.19 -4.49 1.80e+00 3.09e-01 6.21e+00 angle pdb=" C GLN B 396 " pdb=" N GLN B 397 " pdb=" CA GLN B 397 " ideal model delta sigma weight residual 121.70 126.16 -4.46 1.80e+00 3.09e-01 6.14e+00 angle pdb=" N VAL B 169 " pdb=" CA VAL B 169 " pdb=" C VAL B 169 " ideal model delta sigma weight residual 113.47 111.16 2.31 1.01e+00 9.80e-01 5.25e+00 ... (remaining 12993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.66: 5074 14.66 - 29.33: 498 29.33 - 43.99: 134 43.99 - 58.66: 24 58.66 - 73.32: 16 Dihedral angle restraints: 5746 sinusoidal: 2336 harmonic: 3410 Sorted by residual: dihedral pdb=" CA VAL B 483 " pdb=" C VAL B 483 " pdb=" N VAL B 484 " pdb=" CA VAL B 484 " ideal model delta harmonic sigma weight residual 180.00 162.48 17.52 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA VAL A 483 " pdb=" C VAL A 483 " pdb=" N VAL A 484 " pdb=" CA VAL A 484 " ideal model delta harmonic sigma weight residual 180.00 162.62 17.38 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CG ARG B 540 " pdb=" CD ARG B 540 " pdb=" NE ARG B 540 " pdb=" CZ ARG B 540 " ideal model delta sinusoidal sigma weight residual -90.00 -130.89 40.89 2 1.50e+01 4.44e-03 9.14e+00 ... (remaining 5743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 771 0.030 - 0.059: 406 0.059 - 0.089: 157 0.089 - 0.119: 60 0.119 - 0.148: 32 Chirality restraints: 1426 Sorted by residual: chirality pdb=" CB ILE B 278 " pdb=" CA ILE B 278 " pdb=" CG1 ILE B 278 " pdb=" CG2 ILE B 278 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CB ILE A 278 " pdb=" CA ILE A 278 " pdb=" CG1 ILE A 278 " pdb=" CG2 ILE A 278 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA ILE A 529 " pdb=" N ILE A 529 " pdb=" C ILE A 529 " pdb=" CB ILE A 529 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 1423 not shown) Planarity restraints: 1668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 190 " -0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO B 191 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 191 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 191 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 190 " 0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO A 191 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 191 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 191 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 231 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.44e+00 pdb=" N PRO A 232 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 232 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 232 " 0.017 5.00e-02 4.00e+02 ... (remaining 1665 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2281 2.78 - 3.31: 8750 3.31 - 3.84: 16605 3.84 - 4.37: 20500 4.37 - 4.90: 33708 Nonbonded interactions: 81844 Sorted by model distance: nonbonded pdb=" O THR A 185 " pdb=" OH TYR A 412 " model vdw 2.253 2.440 nonbonded pdb=" O THR B 185 " pdb=" OH TYR B 412 " model vdw 2.256 2.440 nonbonded pdb=" OG SER A 431 " pdb=" OD1 ASN A 433 " model vdw 2.265 2.440 nonbonded pdb=" OG SER B 431 " pdb=" OD1 ASN B 433 " model vdw 2.265 2.440 nonbonded pdb=" OD1 ASP A 301 " pdb=" OG1 THR A 304 " model vdw 2.273 2.440 ... (remaining 81839 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=0.62 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 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: 4.130 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.250 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 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 : 0.003 0.031 9592 Z= 0.215 Angle : 0.513 6.122 12998 Z= 0.274 Chirality : 0.045 0.148 1426 Planarity : 0.003 0.030 1668 Dihedral : 13.471 73.321 3542 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: -0.63 (0.23), residues: 1150 helix: -0.69 (0.23), residues: 388 sheet: 0.20 (0.47), residues: 142 loop : -0.26 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 344 HIS 0.003 0.001 HIS B 208 PHE 0.009 0.001 PHE A 11 TYR 0.008 0.001 TYR A 464 ARG 0.001 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8543 (pm20) cc_final: 0.8293 (pm20) REVERT: A 19 ASN cc_start: 0.8463 (t0) cc_final: 0.8248 (t0) REVERT: A 132 GLN cc_start: 0.8494 (mp10) cc_final: 0.7930 (mp10) REVERT: A 233 MET cc_start: 0.9133 (mtm) cc_final: 0.8891 (mtm) REVERT: A 261 GLN cc_start: 0.8713 (pt0) cc_final: 0.8181 (pm20) REVERT: A 401 ASP cc_start: 0.8650 (m-30) cc_final: 0.8080 (t0) REVERT: A 564 MET cc_start: 0.7545 (mmp) cc_final: 0.6731 (tpt) REVERT: B 18 GLU cc_start: 0.8538 (pm20) cc_final: 0.8296 (pm20) REVERT: B 19 ASN cc_start: 0.8466 (t0) cc_final: 0.8250 (t0) REVERT: B 132 GLN cc_start: 0.8488 (mp10) cc_final: 0.7931 (mp10) REVERT: B 233 MET cc_start: 0.9148 (mtm) cc_final: 0.8909 (mtm) REVERT: B 261 GLN cc_start: 0.8710 (pt0) cc_final: 0.8186 (pm20) REVERT: B 564 MET cc_start: 0.7572 (mmp) cc_final: 0.6684 (tpt) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 1.5971 time to fit residues: 192.6389 Evaluate side-chains 67 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 0.0970 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 103 optimal weight: 0.0050 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS A 442 HIS A 553 GLN B 240 HIS B 442 HIS B 553 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 9592 Z= 0.147 Angle : 0.450 4.943 12998 Z= 0.241 Chirality : 0.042 0.153 1426 Planarity : 0.003 0.027 1668 Dihedral : 3.927 14.702 1252 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.77 % Allowed : 6.83 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.17 (0.25), residues: 1150 helix: 0.64 (0.26), residues: 394 sheet: -0.15 (0.46), residues: 140 loop : -0.05 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 183 HIS 0.001 0.000 HIS A 208 PHE 0.009 0.001 PHE A 506 TYR 0.015 0.001 TYR A 112 ARG 0.004 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.8613 (pm20) cc_final: 0.8378 (pm20) REVERT: A 159 GLU cc_start: 0.8851 (mp0) cc_final: 0.8550 (pm20) REVERT: A 261 GLN cc_start: 0.8691 (pt0) cc_final: 0.8210 (pm20) REVERT: A 401 ASP cc_start: 0.8650 (m-30) cc_final: 0.8045 (t0) REVERT: A 564 MET cc_start: 0.7276 (mmp) cc_final: 0.6358 (tmm) REVERT: B 18 GLU cc_start: 0.8613 (pm20) cc_final: 0.8378 (pm20) REVERT: B 159 GLU cc_start: 0.8864 (mp0) cc_final: 0.8551 (pm20) REVERT: B 261 GLN cc_start: 0.8680 (pt0) cc_final: 0.8199 (pm20) REVERT: B 401 ASP cc_start: 0.8637 (m-30) cc_final: 0.8031 (t0) REVERT: B 564 MET cc_start: 0.7223 (mmp) cc_final: 0.6496 (tpt) REVERT: B 574 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8507 (pptt) REVERT: B 586 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8451 (mttp) outliers start: 8 outliers final: 2 residues processed: 80 average time/residue: 1.4623 time to fit residues: 124.9135 Evaluate side-chains 68 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 586 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS B 240 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9592 Z= 0.283 Angle : 0.486 4.972 12998 Z= 0.260 Chirality : 0.044 0.150 1426 Planarity : 0.003 0.025 1668 Dihedral : 4.055 15.152 1252 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.19 % Allowed : 9.71 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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 (0.25), residues: 1150 helix: 1.25 (0.27), residues: 394 sheet: -0.16 (0.44), residues: 138 loop : 0.11 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 316 HIS 0.003 0.001 HIS A 442 PHE 0.019 0.001 PHE A 506 TYR 0.011 0.001 TYR B 112 ARG 0.003 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8946 (m-30) cc_final: 0.8421 (p0) REVERT: A 401 ASP cc_start: 0.8709 (m-30) cc_final: 0.8119 (t0) REVERT: A 506 PHE cc_start: 0.8977 (t80) cc_final: 0.8727 (t80) REVERT: A 564 MET cc_start: 0.7388 (mmp) cc_final: 0.6504 (tmm) REVERT: B 173 ASP cc_start: 0.8951 (m-30) cc_final: 0.8421 (p0) REVERT: B 401 ASP cc_start: 0.8674 (m-30) cc_final: 0.8093 (t0) REVERT: B 506 PHE cc_start: 0.8977 (t80) cc_final: 0.8729 (t80) REVERT: B 564 MET cc_start: 0.7357 (mmp) cc_final: 0.6708 (tpt) outliers start: 2 outliers final: 0 residues processed: 66 average time/residue: 1.3675 time to fit residues: 97.4237 Evaluate side-chains 65 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 104 optimal weight: 0.0370 chunk 110 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 overall best weight: 0.6862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS B 240 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9592 Z= 0.158 Angle : 0.431 4.823 12998 Z= 0.230 Chirality : 0.042 0.149 1426 Planarity : 0.003 0.025 1668 Dihedral : 3.808 15.131 1252 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.67 % Allowed : 10.29 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.77 (0.25), residues: 1150 helix: 1.49 (0.27), residues: 394 sheet: -0.37 (0.43), residues: 138 loop : 0.19 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 316 HIS 0.001 0.000 HIS A 208 PHE 0.010 0.001 PHE A 506 TYR 0.012 0.001 TYR B 112 ARG 0.002 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8456 (mp10) cc_final: 0.7631 (mp10) REVERT: A 173 ASP cc_start: 0.8933 (m-30) cc_final: 0.8490 (p0) REVERT: A 471 TYR cc_start: 0.8752 (p90) cc_final: 0.8347 (p90) REVERT: A 506 PHE cc_start: 0.8955 (t80) cc_final: 0.8635 (t80) REVERT: A 564 MET cc_start: 0.7274 (mmp) cc_final: 0.6400 (tmm) REVERT: B 132 GLN cc_start: 0.8463 (mp10) cc_final: 0.7644 (mp10) REVERT: B 173 ASP cc_start: 0.8935 (m-30) cc_final: 0.8490 (p0) REVERT: B 471 TYR cc_start: 0.8756 (p90) cc_final: 0.8347 (p90) REVERT: B 506 PHE cc_start: 0.8953 (t80) cc_final: 0.8639 (t80) REVERT: B 564 MET cc_start: 0.7297 (mmp) cc_final: 0.6416 (tmm) outliers start: 7 outliers final: 4 residues processed: 64 average time/residue: 1.3314 time to fit residues: 91.9181 Evaluate side-chains 66 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 508 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 98 optimal weight: 0.0970 chunk 27 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS B 240 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9592 Z= 0.187 Angle : 0.436 4.827 12998 Z= 0.233 Chirality : 0.042 0.145 1426 Planarity : 0.003 0.025 1668 Dihedral : 3.759 14.541 1252 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.25 % Allowed : 9.81 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.90 (0.25), residues: 1150 helix: 1.65 (0.27), residues: 396 sheet: -0.45 (0.43), residues: 138 loop : 0.26 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 316 HIS 0.002 0.001 HIS B 442 PHE 0.011 0.001 PHE A 506 TYR 0.010 0.001 TYR A 112 ARG 0.002 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7256 (mtm) REVERT: A 132 GLN cc_start: 0.8473 (mp10) cc_final: 0.7632 (mp10) REVERT: A 173 ASP cc_start: 0.8936 (m-30) cc_final: 0.8502 (p0) REVERT: A 506 PHE cc_start: 0.8959 (t80) cc_final: 0.8705 (t80) REVERT: A 539 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8233 (mt) REVERT: A 564 MET cc_start: 0.7309 (mmp) cc_final: 0.6431 (tmm) REVERT: B 132 GLN cc_start: 0.8474 (mp10) cc_final: 0.7633 (mp10) REVERT: B 173 ASP cc_start: 0.8954 (m-30) cc_final: 0.8493 (p0) REVERT: B 449 LYS cc_start: 0.9045 (ptpt) cc_final: 0.8700 (ptmm) REVERT: B 471 TYR cc_start: 0.8806 (p90) cc_final: 0.8430 (p90) REVERT: B 506 PHE cc_start: 0.8953 (t80) cc_final: 0.8655 (t80) REVERT: B 539 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8202 (mm) REVERT: B 564 MET cc_start: 0.7324 (mmp) cc_final: 0.6342 (tmm) outliers start: 13 outliers final: 0 residues processed: 75 average time/residue: 1.3327 time to fit residues: 107.6843 Evaluate side-chains 67 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain B residue 539 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 91 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9592 Z= 0.260 Angle : 0.466 4.889 12998 Z= 0.250 Chirality : 0.043 0.142 1426 Planarity : 0.003 0.027 1668 Dihedral : 3.912 14.765 1252 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.44 % Allowed : 10.77 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.88 (0.25), residues: 1150 helix: 1.63 (0.27), residues: 398 sheet: -0.44 (0.43), residues: 138 loop : 0.24 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 316 HIS 0.003 0.001 HIS A 442 PHE 0.012 0.001 PHE B 506 TYR 0.009 0.001 TYR B 226 ARG 0.005 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 66 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8436 (mp10) cc_final: 0.7537 (mp10) REVERT: A 173 ASP cc_start: 0.8970 (m-30) cc_final: 0.8429 (p0) REVERT: A 506 PHE cc_start: 0.9045 (t80) cc_final: 0.8797 (t80) REVERT: A 564 MET cc_start: 0.7377 (mmp) cc_final: 0.6484 (tmm) REVERT: B 132 GLN cc_start: 0.8434 (mp10) cc_final: 0.7536 (mp10) REVERT: B 173 ASP cc_start: 0.8973 (m-30) cc_final: 0.8427 (p0) REVERT: B 449 LYS cc_start: 0.9041 (ptpt) cc_final: 0.8684 (ptmm) REVERT: B 506 PHE cc_start: 0.9045 (t80) cc_final: 0.8801 (t80) REVERT: B 539 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8219 (mm) REVERT: B 564 MET cc_start: 0.7383 (mmp) cc_final: 0.6506 (tmm) outliers start: 15 outliers final: 5 residues processed: 74 average time/residue: 1.4083 time to fit residues: 112.3304 Evaluate side-chains 69 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 539 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.0670 chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 61 optimal weight: 0.0980 chunk 109 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.0324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS B 240 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9592 Z= 0.208 Angle : 0.452 4.850 12998 Z= 0.242 Chirality : 0.043 0.141 1426 Planarity : 0.003 0.029 1668 Dihedral : 3.878 14.992 1252 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.25 % Allowed : 10.67 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.89 (0.25), residues: 1150 helix: 1.66 (0.27), residues: 398 sheet: -0.46 (0.43), residues: 138 loop : 0.24 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 316 HIS 0.002 0.001 HIS B 442 PHE 0.010 0.001 PHE A 506 TYR 0.010 0.001 TYR A 112 ARG 0.004 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.7294 (mtm) REVERT: A 132 GLN cc_start: 0.8435 (mp10) cc_final: 0.7597 (mp10) REVERT: A 173 ASP cc_start: 0.8945 (m-30) cc_final: 0.8510 (p0) REVERT: A 401 ASP cc_start: 0.8658 (m-30) cc_final: 0.8023 (t0) REVERT: A 471 TYR cc_start: 0.8782 (p90) cc_final: 0.8436 (p90) REVERT: A 506 PHE cc_start: 0.9014 (t80) cc_final: 0.8724 (t80) REVERT: A 564 MET cc_start: 0.7347 (mmp) cc_final: 0.6343 (tmm) REVERT: B 132 GLN cc_start: 0.8432 (mp10) cc_final: 0.7595 (mp10) REVERT: B 173 ASP cc_start: 0.8946 (m-30) cc_final: 0.8508 (p0) REVERT: B 401 ASP cc_start: 0.8638 (m-30) cc_final: 0.8033 (t0) REVERT: B 449 LYS cc_start: 0.9036 (ptpt) cc_final: 0.8718 (ptmm) REVERT: B 471 TYR cc_start: 0.8781 (p90) cc_final: 0.8431 (p90) REVERT: B 506 PHE cc_start: 0.9013 (t80) cc_final: 0.8729 (t80) REVERT: B 564 MET cc_start: 0.7299 (mmp) cc_final: 0.6325 (tmm) outliers start: 13 outliers final: 5 residues processed: 72 average time/residue: 1.3014 time to fit residues: 101.1987 Evaluate side-chains 74 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain B residue 389 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 5.9990 chunk 65 optimal weight: 0.3980 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 69 optimal weight: 0.2980 chunk 74 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS B 240 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9592 Z= 0.147 Angle : 0.433 5.292 12998 Z= 0.232 Chirality : 0.042 0.140 1426 Planarity : 0.003 0.029 1668 Dihedral : 3.725 14.669 1252 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.48 % Allowed : 11.54 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1150 helix: 1.77 (0.27), residues: 396 sheet: -0.43 (0.43), residues: 138 loop : 0.30 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 183 HIS 0.001 0.000 HIS B 240 PHE 0.008 0.001 PHE B 94 TYR 0.011 0.001 TYR A 112 ARG 0.002 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8437 (mp10) cc_final: 0.7590 (mp10) REVERT: A 173 ASP cc_start: 0.8939 (m-30) cc_final: 0.8495 (p0) REVERT: A 401 ASP cc_start: 0.8638 (m-30) cc_final: 0.8023 (t0) REVERT: A 471 TYR cc_start: 0.8736 (p90) cc_final: 0.8384 (p90) REVERT: A 506 PHE cc_start: 0.8969 (t80) cc_final: 0.8663 (t80) REVERT: A 564 MET cc_start: 0.7345 (mmp) cc_final: 0.6361 (tmm) REVERT: B 132 GLN cc_start: 0.8437 (mp10) cc_final: 0.7616 (mp10) REVERT: B 173 ASP cc_start: 0.8941 (m-30) cc_final: 0.8493 (p0) REVERT: B 401 ASP cc_start: 0.8642 (m-30) cc_final: 0.8020 (t0) REVERT: B 449 LYS cc_start: 0.9012 (ptpt) cc_final: 0.8674 (ptmm) REVERT: B 471 TYR cc_start: 0.8734 (p90) cc_final: 0.8368 (p90) REVERT: B 506 PHE cc_start: 0.8973 (t80) cc_final: 0.8668 (t80) REVERT: B 564 MET cc_start: 0.7334 (mmp) cc_final: 0.6381 (tmm) outliers start: 5 outliers final: 3 residues processed: 73 average time/residue: 1.3655 time to fit residues: 107.3539 Evaluate side-chains 71 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain B residue 389 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 0.0470 chunk 92 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9592 Z= 0.147 Angle : 0.434 5.841 12998 Z= 0.231 Chirality : 0.042 0.141 1426 Planarity : 0.003 0.030 1668 Dihedral : 3.671 14.150 1252 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.77 % Allowed : 11.35 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.25), residues: 1150 helix: 1.77 (0.27), residues: 398 sheet: -0.34 (0.43), residues: 138 loop : 0.32 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 316 HIS 0.001 0.000 HIS A 240 PHE 0.008 0.001 PHE B 94 TYR 0.010 0.001 TYR B 112 ARG 0.002 0.000 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8406 (mp10) cc_final: 0.7559 (mp10) REVERT: A 173 ASP cc_start: 0.8929 (m-30) cc_final: 0.8490 (p0) REVERT: A 401 ASP cc_start: 0.8626 (m-30) cc_final: 0.8030 (t0) REVERT: A 449 LYS cc_start: 0.8992 (ptpt) cc_final: 0.8602 (ptmm) REVERT: A 471 TYR cc_start: 0.8762 (p90) cc_final: 0.8398 (p90) REVERT: A 506 PHE cc_start: 0.8922 (t80) cc_final: 0.8593 (t80) REVERT: A 564 MET cc_start: 0.7346 (mmp) cc_final: 0.6352 (tmm) REVERT: B 132 GLN cc_start: 0.8404 (mp10) cc_final: 0.7558 (mp10) REVERT: B 173 ASP cc_start: 0.8940 (m-30) cc_final: 0.8490 (p0) REVERT: B 401 ASP cc_start: 0.8621 (m-30) cc_final: 0.8020 (t0) REVERT: B 449 LYS cc_start: 0.8991 (ptpt) cc_final: 0.8599 (ptmm) REVERT: B 471 TYR cc_start: 0.8763 (p90) cc_final: 0.8392 (p90) REVERT: B 506 PHE cc_start: 0.8924 (t80) cc_final: 0.8612 (t80) REVERT: B 543 MET cc_start: 0.8371 (mtm) cc_final: 0.7807 (ptp) REVERT: B 550 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.8200 (p0) REVERT: B 564 MET cc_start: 0.7345 (mmp) cc_final: 0.6362 (tmm) outliers start: 8 outliers final: 4 residues processed: 72 average time/residue: 1.3255 time to fit residues: 102.9496 Evaluate side-chains 72 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 550 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS B 240 HIS ** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 9592 Z= 0.398 Angle : 0.537 6.128 12998 Z= 0.287 Chirality : 0.046 0.143 1426 Planarity : 0.003 0.034 1668 Dihedral : 4.195 14.981 1252 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.58 % Allowed : 11.83 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.91 (0.25), residues: 1150 helix: 1.63 (0.27), residues: 398 sheet: -0.41 (0.43), residues: 138 loop : 0.27 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 316 HIS 0.005 0.001 HIS B 442 PHE 0.015 0.001 PHE B 506 TYR 0.011 0.001 TYR A 226 ARG 0.004 0.000 ARG A 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 GLN cc_start: 0.8391 (mp10) cc_final: 0.7530 (mp10) REVERT: A 173 ASP cc_start: 0.8967 (m-30) cc_final: 0.8447 (p0) REVERT: A 401 ASP cc_start: 0.8651 (m-30) cc_final: 0.8102 (t0) REVERT: A 449 LYS cc_start: 0.9010 (ptpt) cc_final: 0.8673 (ptmm) REVERT: A 564 MET cc_start: 0.7422 (mmp) cc_final: 0.6432 (tmm) REVERT: B 132 GLN cc_start: 0.8389 (mp10) cc_final: 0.7528 (mp10) REVERT: B 173 ASP cc_start: 0.8981 (m-30) cc_final: 0.8460 (p0) REVERT: B 401 ASP cc_start: 0.8649 (m-30) cc_final: 0.8102 (t0) REVERT: B 449 LYS cc_start: 0.9008 (ptpt) cc_final: 0.8654 (ptmm) REVERT: B 564 MET cc_start: 0.7435 (mmp) cc_final: 0.6462 (tmm) outliers start: 6 outliers final: 2 residues processed: 67 average time/residue: 1.3672 time to fit residues: 98.5259 Evaluate side-chains 70 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 508 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 65 optimal weight: 0.0000 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.075801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.062199 restraints weight = 20965.913| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.74 r_work: 0.2826 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9592 Z= 0.166 Angle : 0.458 5.924 12998 Z= 0.243 Chirality : 0.042 0.143 1426 Planarity : 0.003 0.029 1668 Dihedral : 3.891 15.068 1252 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.48 % Allowed : 11.83 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.25), residues: 1150 helix: 1.71 (0.27), residues: 400 sheet: -0.32 (0.43), residues: 138 loop : 0.31 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 316 HIS 0.001 0.000 HIS A 208 PHE 0.008 0.001 PHE A 506 TYR 0.010 0.001 TYR B 112 ARG 0.003 0.000 ARG A 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2890.07 seconds wall clock time: 53 minutes 20.57 seconds (3200.57 seconds total)