Starting phenix.real_space_refine on Mon Mar 11 13:02:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z29_14458/03_2024/7z29_14458_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z29_14458/03_2024/7z29_14458.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z29_14458/03_2024/7z29_14458_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z29_14458/03_2024/7z29_14458_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z29_14458/03_2024/7z29_14458_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z29_14458/03_2024/7z29_14458.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z29_14458/03_2024/7z29_14458.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z29_14458/03_2024/7z29_14458_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z29_14458/03_2024/7z29_14458_updated.pdb" } resolution = 3.38 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 35 5.49 5 S 12 5.16 5 C 5264 2.51 5 N 1388 2.21 5 O 1608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 203": "OE1" <-> "OE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A GLU 378": "OE1" <-> "OE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B GLU 122": "OE1" <-> "OE2" 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: 8307 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4268 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 494} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3298 Classifications: {'peptide': 405} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 30, 'TRANS': 374} Chain breaks: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 721 Classifications: {'DNA': 34, 'RNA': 2} Modifications used: {'5*END': 1, 'rna3p': 2} Link IDs: {'rna3p': 35} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan2': 1, ' DA%5*END:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'NVP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.14, per 1000 atoms: 0.62 Number of scatterers: 8307 At special positions: 0 Unit cell: (98.94, 109.61, 95.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 35 15.00 O 1608 8.00 N 1388 7.00 C 5264 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: 3.36 Conformation dependent library (CDL) restraints added in 1.6 seconds 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1766 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 9 sheets defined 33.9% alpha, 12.8% beta 13 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 31 through 43 removed outlier: 4.476A pdb=" N ILE A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 114 through 117 No H-bonds generated for 'chain 'A' and resid 114 through 117' Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.969A pdb=" N LYS A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 127' Processing helix chain 'A' and resid 156 through 174 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 195 through 211 Processing helix chain 'A' and resid 254 through 269 removed outlier: 4.445A pdb=" N GLN A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.809A pdb=" N LEU A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 310 Processing helix chain 'A' and resid 364 through 382 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 476 through 487 removed outlier: 4.220A pdb=" N ILE A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 516 through 527 removed outlier: 3.578A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 552 removed outlier: 3.612A pdb=" N GLU A 546 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP A 549 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 44 removed outlier: 4.121A pdb=" N LEU B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU B 44 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 88 removed outlier: 5.543A pdb=" N ASP B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TRP B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 102 removed outlier: 3.527A pdb=" N LYS B 101 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 102 " --> pdb=" O GLY B 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 98 through 102' Processing helix chain 'B' and resid 112 through 115 Processing helix chain 'B' and resid 124 through 126 No H-bonds generated for 'chain 'B' and resid 124 through 126' Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 154 through 174 removed outlier: 4.081A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 195 through 211 removed outlier: 3.802A pdb=" N THR B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 254 through 270 removed outlier: 4.186A pdb=" N GLN B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE B 270 " --> pdb=" O TRP B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 311 Processing helix chain 'B' and resid 365 through 382 Processing helix chain 'B' and resid 395 through 405 removed outlier: 5.476A pdb=" N THR B 403 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N GLU B 404 " --> pdb=" O THR B 400 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TYR B 405 " --> pdb=" O TRP B 401 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 105 through 110 Processing sheet with id= B, first strand: chain 'A' and resid 129 through 131 Processing sheet with id= C, first strand: chain 'A' and resid 227 through 229 Processing sheet with id= D, first strand: chain 'A' and resid 414 through 416 removed outlier: 6.573A pdb=" N PHE A 389 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS A 390 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU A 328 " --> pdb=" O GLN A 340 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN A 340 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 464 through 470 removed outlier: 3.968A pdb=" N GLY A 456 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A 443 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU A 438 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LYS A 530 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ILE A 495 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TYR A 532 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N THR A 497 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA A 534 " --> pdb=" O THR A 497 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 61 through 64 Processing sheet with id= G, first strand: chain 'B' and resid 105 through 110 removed outlier: 3.532A pdb=" N SER B 105 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER B 191 " --> pdb=" O SER B 105 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 129 through 132 Processing sheet with id= I, first strand: chain 'B' and resid 413 through 416 removed outlier: 3.521A pdb=" N ALA B 327 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR B 339 " --> pdb=" O GLY B 352 " (cutoff:3.500A) 251 hydrogen bonds defined for protein. 696 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 2.51 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1309 1.31 - 1.44: 2388 1.44 - 1.56: 4808 1.56 - 1.68: 69 1.68 - 1.81: 21 Bond restraints: 8595 Sorted by residual: bond pdb=" C2 OMC E 2 " pdb=" N3 OMC E 2 " ideal model delta sigma weight residual 1.491 1.347 0.144 2.00e-02 2.50e+03 5.21e+01 bond pdb=" C2 OMC E 4 " pdb=" N3 OMC E 4 " ideal model delta sigma weight residual 1.491 1.350 0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" N1 OMC E 2 " pdb=" C6 OMC E 2 " ideal model delta sigma weight residual 1.455 1.336 0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" N1 OMC E 4 " pdb=" C6 OMC E 4 " ideal model delta sigma weight residual 1.455 1.338 0.117 2.00e-02 2.50e+03 3.45e+01 bond pdb=" C4 OMC E 4 " pdb=" C5 OMC E 4 " ideal model delta sigma weight residual 1.484 1.378 0.106 2.00e-02 2.50e+03 2.83e+01 ... (remaining 8590 not shown) Histogram of bond angle deviations from ideal: 59.63 - 74.59: 3 74.59 - 89.56: 0 89.56 - 104.52: 286 104.52 - 119.49: 7341 119.49 - 134.45: 4214 Bond angle restraints: 11844 Sorted by residual: angle pdb=" C5' DG E 19 " pdb=" C4' DG E 19 " pdb=" O4' DG E 19 " ideal model delta sigma weight residual 109.40 121.13 -11.73 1.50e+00 4.44e-01 6.12e+01 angle pdb=" N PRO A 412 " pdb=" CA PRO A 412 " pdb=" C PRO A 412 " ideal model delta sigma weight residual 112.47 126.72 -14.25 2.06e+00 2.36e-01 4.79e+01 angle pdb=" C5' DC E 3 " pdb=" C4' DC E 3 " pdb=" O4' DC E 3 " ideal model delta sigma weight residual 109.40 119.40 -10.00 1.50e+00 4.44e-01 4.45e+01 angle pdb=" CA GLY B 333 " pdb=" C GLY B 333 " pdb=" O GLY B 333 " ideal model delta sigma weight residual 122.24 117.62 4.62 8.70e-01 1.32e+00 2.82e+01 angle pdb=" C THR B 131 " pdb=" N ILE B 132 " pdb=" CA ILE B 132 " ideal model delta sigma weight residual 122.59 118.81 3.78 7.20e-01 1.93e+00 2.76e+01 ... (remaining 11839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 4319 17.69 - 35.38: 550 35.38 - 53.07: 128 53.07 - 70.76: 45 70.76 - 88.46: 12 Dihedral angle restraints: 5054 sinusoidal: 2321 harmonic: 2733 Sorted by residual: dihedral pdb=" C TYR A 183 " pdb=" N TYR A 183 " pdb=" CA TYR A 183 " pdb=" CB TYR A 183 " ideal model delta harmonic sigma weight residual -122.60 -111.33 -11.27 0 2.50e+00 1.60e-01 2.03e+01 dihedral pdb=" C LYS B 424 " pdb=" N LYS B 424 " pdb=" CA LYS B 424 " pdb=" CB LYS B 424 " ideal model delta harmonic sigma weight residual -122.60 -133.72 11.12 0 2.50e+00 1.60e-01 1.98e+01 dihedral pdb=" CA GLU B 44 " pdb=" C GLU B 44 " pdb=" N GLY B 45 " pdb=" CA GLY B 45 " ideal model delta harmonic sigma weight residual 180.00 159.38 20.62 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 5051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1104 0.074 - 0.148: 148 0.148 - 0.222: 28 0.222 - 0.297: 10 0.297 - 0.371: 6 Chirality restraints: 1296 Sorted by residual: chirality pdb=" CA GLU B 415 " pdb=" N GLU B 415 " pdb=" C GLU B 415 " pdb=" CB GLU B 415 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CA TYR A 183 " pdb=" N TYR A 183 " pdb=" C TYR A 183 " pdb=" CB TYR A 183 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA LYS B 101 " pdb=" N LYS B 101 " pdb=" C LYS B 101 " pdb=" CB LYS B 101 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.06e+00 ... (remaining 1293 not shown) Planarity restraints: 1373 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC E 4 " 0.014 2.00e-02 2.50e+03 6.25e-01 8.78e+03 pdb=" C4' OMC E 4 " 0.438 2.00e-02 2.50e+03 pdb=" O4' OMC E 4 " 0.620 2.00e-02 2.50e+03 pdb=" C3' OMC E 4 " -0.617 2.00e-02 2.50e+03 pdb=" O3' OMC E 4 " -0.683 2.00e-02 2.50e+03 pdb=" C2' OMC E 4 " -0.133 2.00e-02 2.50e+03 pdb=" O2' OMC E 4 " 1.069 2.00e-02 2.50e+03 pdb=" C1' OMC E 4 " 0.228 2.00e-02 2.50e+03 pdb=" N1 OMC E 4 " -0.935 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC E 2 " 0.018 2.00e-02 2.50e+03 6.24e-01 8.76e+03 pdb=" C4' OMC E 2 " 0.454 2.00e-02 2.50e+03 pdb=" O4' OMC E 2 " 0.634 2.00e-02 2.50e+03 pdb=" C3' OMC E 2 " -0.609 2.00e-02 2.50e+03 pdb=" O3' OMC E 2 " -0.679 2.00e-02 2.50e+03 pdb=" C2' OMC E 2 " -0.144 2.00e-02 2.50e+03 pdb=" O2' OMC E 2 " 1.046 2.00e-02 2.50e+03 pdb=" C1' OMC E 2 " 0.226 2.00e-02 2.50e+03 pdb=" N1 OMC E 2 " -0.947 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 307 " 0.465 9.50e-02 1.11e+02 2.09e-01 2.66e+01 pdb=" NE ARG A 307 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG A 307 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 307 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 307 " 0.016 2.00e-02 2.50e+03 ... (remaining 1370 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2412 2.82 - 3.34: 7287 3.34 - 3.86: 13500 3.86 - 4.38: 15909 4.38 - 4.90: 26313 Nonbonded interactions: 65421 Sorted by model distance: nonbonded pdb=" O LYS B 323 " pdb=" NZ LYS B 385 " model vdw 2.304 2.520 nonbonded pdb=" OH TYR A 457 " pdb=" OD2 ASP A 488 " model vdw 2.361 2.440 nonbonded pdb=" NZ LYS A 104 " pdb=" O LEU A 193 " model vdw 2.364 2.520 nonbonded pdb=" OD1 ASP B 17 " pdb=" N GLY B 18 " model vdw 2.369 2.520 nonbonded pdb=" OE1 GLN A 547 " pdb=" OG1 THR B 286 " model vdw 2.372 2.440 ... (remaining 65416 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.970 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.950 Find NCS groups from input model: 0.220 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: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 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 : 0.007 0.144 8595 Z= 0.427 Angle : 0.824 14.254 11844 Z= 0.521 Chirality : 0.061 0.371 1296 Planarity : 0.025 0.625 1373 Dihedral : 17.163 88.455 3288 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.04 % Favored : 96.85 % Rotamer: Outliers : 1.96 % Allowed : 1.96 % Favored : 96.09 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.28), residues: 921 helix: 0.95 (0.31), residues: 325 sheet: -1.19 (0.39), residues: 171 loop : -0.85 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 402 HIS 0.003 0.001 HIS A 235 PHE 0.007 0.001 PHE A 389 TYR 0.030 0.002 TYR A 319 ARG 0.004 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 0.962 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 4 residues processed: 132 average time/residue: 0.1998 time to fit residues: 36.4663 Evaluate side-chains 99 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 30.0000 chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 29 optimal weight: 0.0980 chunk 45 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 overall best weight: 4.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8595 Z= 0.296 Angle : 0.760 13.314 11844 Z= 0.426 Chirality : 0.045 0.249 1296 Planarity : 0.007 0.127 1373 Dihedral : 17.305 81.214 1385 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.69 % Favored : 96.09 % Rotamer: Outliers : 1.10 % Allowed : 11.25 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.27), residues: 921 helix: 0.81 (0.30), residues: 325 sheet: -1.12 (0.40), residues: 163 loop : -1.05 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 402 HIS 0.004 0.001 HIS A 235 PHE 0.009 0.002 PHE B 130 TYR 0.017 0.002 TYR A 339 ARG 0.003 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: A 182 GLN cc_start: 0.7524 (pt0) cc_final: 0.7234 (pt0) REVERT: A 545 ASN cc_start: 0.6700 (t0) cc_final: 0.6495 (t0) REVERT: B 102 LYS cc_start: 0.7367 (mppt) cc_final: 0.6856 (mppt) outliers start: 9 outliers final: 7 residues processed: 103 average time/residue: 0.2167 time to fit residues: 31.0675 Evaluate side-chains 102 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 59 optimal weight: 0.0870 chunk 24 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 77 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 overall best weight: 3.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8595 Z= 0.212 Angle : 0.688 14.147 11844 Z= 0.399 Chirality : 0.043 0.161 1296 Planarity : 0.006 0.116 1373 Dihedral : 17.363 85.552 1385 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.28 % Favored : 97.61 % Rotamer: Outliers : 1.96 % Allowed : 13.69 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.28), residues: 921 helix: 0.98 (0.30), residues: 325 sheet: -1.19 (0.39), residues: 177 loop : -0.91 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 406 HIS 0.003 0.000 HIS A 235 PHE 0.008 0.001 PHE B 416 TYR 0.013 0.002 TYR A 339 ARG 0.003 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 182 GLN cc_start: 0.7567 (pt0) cc_final: 0.7330 (pt0) REVERT: B 382 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.7899 (mp) outliers start: 16 outliers final: 12 residues processed: 109 average time/residue: 0.1917 time to fit residues: 29.2372 Evaluate side-chains 102 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8595 Z= 0.253 Angle : 0.706 13.847 11844 Z= 0.407 Chirality : 0.043 0.234 1296 Planarity : 0.006 0.116 1373 Dihedral : 16.966 77.550 1385 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.26 % Favored : 96.63 % Rotamer: Outliers : 3.06 % Allowed : 15.40 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.27), residues: 921 helix: 0.88 (0.29), residues: 321 sheet: -1.39 (0.39), residues: 175 loop : -0.99 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 406 HIS 0.003 0.001 HIS A 235 PHE 0.008 0.001 PHE B 130 TYR 0.023 0.002 TYR A 232 ARG 0.002 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 0.861 Fit side-chains revert: symmetry clash REVERT: A 182 GLN cc_start: 0.7536 (pt0) cc_final: 0.7311 (pt0) REVERT: B 382 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.7948 (mp) outliers start: 25 outliers final: 18 residues processed: 118 average time/residue: 0.2037 time to fit residues: 33.5278 Evaluate side-chains 111 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 chunk 69 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN B 255 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8595 Z= 0.305 Angle : 0.731 13.829 11844 Z= 0.419 Chirality : 0.044 0.175 1296 Planarity : 0.006 0.116 1373 Dihedral : 16.911 77.085 1385 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.02 % Favored : 95.87 % Rotamer: Outliers : 3.42 % Allowed : 16.99 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.27), residues: 921 helix: 0.58 (0.29), residues: 326 sheet: -1.40 (0.40), residues: 163 loop : -1.15 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 406 HIS 0.004 0.001 HIS A 235 PHE 0.009 0.002 PHE B 130 TYR 0.024 0.002 TYR B 115 ARG 0.003 0.000 ARG B 125 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 104 time to evaluate : 0.864 Fit side-chains REVERT: B 382 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8044 (mp) outliers start: 28 outliers final: 24 residues processed: 128 average time/residue: 0.2026 time to fit residues: 36.2656 Evaluate side-chains 121 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 92 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8595 Z= 0.250 Angle : 0.704 13.768 11844 Z= 0.406 Chirality : 0.043 0.154 1296 Planarity : 0.006 0.115 1373 Dihedral : 16.654 76.958 1385 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.80 % Favored : 96.09 % Rotamer: Outliers : 3.67 % Allowed : 17.48 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.27), residues: 921 helix: 0.70 (0.29), residues: 321 sheet: -1.48 (0.39), residues: 173 loop : -1.05 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 406 HIS 0.003 0.001 HIS A 235 PHE 0.007 0.001 PHE B 130 TYR 0.021 0.002 TYR A 232 ARG 0.002 0.000 ARG B 125 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 104 time to evaluate : 0.996 Fit side-chains REVERT: B 342 TYR cc_start: 0.7382 (p90) cc_final: 0.7073 (p90) REVERT: B 382 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8035 (mp) outliers start: 30 outliers final: 24 residues processed: 128 average time/residue: 0.1996 time to fit residues: 36.3421 Evaluate side-chains 125 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 100 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 30.0000 chunk 52 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 78 optimal weight: 0.2980 chunk 51 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 42 optimal weight: 30.0000 chunk 36 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 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 480 GLN ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8595 Z= 0.176 Angle : 0.668 13.611 11844 Z= 0.389 Chirality : 0.041 0.155 1296 Planarity : 0.006 0.113 1373 Dihedral : 16.331 77.903 1385 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.50 % Favored : 97.39 % Rotamer: Outliers : 2.57 % Allowed : 18.46 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.28), residues: 921 helix: 1.11 (0.30), residues: 317 sheet: -1.30 (0.39), residues: 175 loop : -0.85 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 406 HIS 0.002 0.001 HIS A 235 PHE 0.006 0.001 PHE B 416 TYR 0.020 0.001 TYR A 232 ARG 0.003 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 0.817 Fit side-chains REVERT: A 215 THR cc_start: 0.8101 (p) cc_final: 0.7899 (p) REVERT: B 342 TYR cc_start: 0.7311 (p90) cc_final: 0.7063 (p90) REVERT: B 382 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.7974 (mp) outliers start: 21 outliers final: 17 residues processed: 114 average time/residue: 0.2001 time to fit residues: 32.0981 Evaluate side-chains 109 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8595 Z= 0.186 Angle : 0.674 13.467 11844 Z= 0.391 Chirality : 0.041 0.178 1296 Planarity : 0.006 0.114 1373 Dihedral : 16.273 77.638 1380 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.93 % Favored : 96.96 % Rotamer: Outliers : 2.44 % Allowed : 19.44 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.28), residues: 921 helix: 1.13 (0.30), residues: 317 sheet: -1.24 (0.39), residues: 175 loop : -0.83 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 406 HIS 0.003 0.001 HIS A 198 PHE 0.005 0.001 PHE B 130 TYR 0.039 0.002 TYR A 501 ARG 0.003 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 0.977 Fit side-chains REVERT: B 342 TYR cc_start: 0.7301 (p90) cc_final: 0.7061 (p90) REVERT: B 382 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.7959 (mp) outliers start: 20 outliers final: 17 residues processed: 112 average time/residue: 0.2029 time to fit residues: 31.9190 Evaluate side-chains 113 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 26 optimal weight: 0.2980 chunk 77 optimal weight: 10.0000 chunk 81 optimal weight: 30.0000 chunk 85 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8595 Z= 0.224 Angle : 0.693 13.389 11844 Z= 0.400 Chirality : 0.042 0.187 1296 Planarity : 0.006 0.115 1373 Dihedral : 16.324 77.320 1380 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.26 % Favored : 96.63 % Rotamer: Outliers : 2.93 % Allowed : 19.32 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.28), residues: 921 helix: 0.93 (0.30), residues: 318 sheet: -1.31 (0.39), residues: 175 loop : -0.90 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 406 HIS 0.003 0.001 HIS A 235 PHE 0.006 0.001 PHE B 130 TYR 0.022 0.002 TYR A 232 ARG 0.003 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 96 time to evaluate : 0.921 Fit side-chains REVERT: B 342 TYR cc_start: 0.7341 (p90) cc_final: 0.7105 (p90) REVERT: B 382 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8021 (mp) outliers start: 24 outliers final: 21 residues processed: 116 average time/residue: 0.2248 time to fit residues: 36.7970 Evaluate side-chains 116 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 88 optimal weight: 0.6980 chunk 76 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8595 Z= 0.182 Angle : 0.680 13.283 11844 Z= 0.392 Chirality : 0.041 0.189 1296 Planarity : 0.006 0.113 1373 Dihedral : 16.221 77.772 1380 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.82 % Favored : 97.07 % Rotamer: Outliers : 2.57 % Allowed : 19.68 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.28), residues: 921 helix: 1.05 (0.30), residues: 318 sheet: -1.26 (0.39), residues: 177 loop : -0.82 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 406 HIS 0.002 0.000 HIS A 235 PHE 0.005 0.001 PHE B 416 TYR 0.022 0.002 TYR A 232 ARG 0.003 0.000 ARG A 356 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 0.957 Fit side-chains REVERT: B 342 TYR cc_start: 0.7327 (p90) cc_final: 0.7094 (p90) REVERT: B 382 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.7963 (mp) outliers start: 21 outliers final: 19 residues processed: 110 average time/residue: 0.1998 time to fit residues: 30.8570 Evaluate side-chains 113 residues out of total 843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 78 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.210315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.166394 restraints weight = 8757.201| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 1.86 r_work: 0.3734 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8595 Z= 0.216 Angle : 0.693 13.226 11844 Z= 0.398 Chirality : 0.042 0.193 1296 Planarity : 0.006 0.114 1373 Dihedral : 16.281 77.414 1380 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.37 % Favored : 96.53 % Rotamer: Outliers : 2.81 % Allowed : 19.56 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.28), residues: 921 helix: 0.95 (0.30), residues: 318 sheet: -1.26 (0.39), residues: 175 loop : -0.89 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 406 HIS 0.003 0.001 HIS A 235 PHE 0.006 0.001 PHE B 130 TYR 0.023 0.002 TYR A 232 ARG 0.003 0.000 ARG A 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1752.69 seconds wall clock time: 32 minutes 42.72 seconds (1962.72 seconds total)