Starting phenix.real_space_refine (version: dev) on Sat Feb 18 18:02:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2d_14462/02_2023/7z2d_14462_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2d_14462/02_2023/7z2d_14462.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2d_14462/02_2023/7z2d_14462_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/7z2d_14462/02_2023/7z2d_14462_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2d_14462/02_2023/7z2d_14462_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2d_14462/02_2023/7z2d_14462.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2d_14462/02_2023/7z2d_14462.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2d_14462/02_2023/7z2d_14462_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2d_14462/02_2023/7z2d_14462_updated.pdb" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "A TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 396": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 8591 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4450 Classifications: {'peptide': 547} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 508} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3393 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 381} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 720 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: 16 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'T27': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.29, per 1000 atoms: 0.62 Number of scatterers: 8591 At special positions: 0 Unit cell: (97, 109.61, 100.88, 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 13 16.00 P 35 15.00 O 1659 8.00 N 1432 7.00 C 5452 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: 3.47 Conformation dependent library (CDL) restraints added in 1.3 seconds 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1804 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 8 sheets defined 33.1% alpha, 12.3% beta 9 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 3.39 Creating SS restraints... Processing helix chain 'A' and resid 34 through 44 Processing helix chain 'A' and resid 78 through 81 No H-bonds generated for 'chain 'A' and resid 78 through 81' 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 113 through 116 Processing helix chain 'A' and resid 125 through 127 No H-bonds generated for 'chain 'A' and resid 125 through 127' Processing helix chain 'A' and resid 156 through 174 Proline residue: A 170 - end of helix removed outlier: 3.741A pdb=" N GLN A 174 " --> pdb=" O PRO A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 211 removed outlier: 3.869A pdb=" N ARG A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N THR A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A 201 " --> pdb=" O GLN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 254 through 269 removed outlier: 4.632A pdb=" N GLN A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.787A pdb=" N LYS A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 277 through 283' Processing helix chain 'A' and resid 297 through 310 removed outlier: 3.637A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 382 removed outlier: 3.568A pdb=" N GLN A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 516 through 527 removed outlier: 3.894A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 4.165A pdb=" N GLU A 546 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 548 " --> pdb=" O ASN A 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 42 removed outlier: 3.793A pdb=" N LEU B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 83 No H-bonds generated for 'chain 'B' and resid 80 through 83' Processing helix chain 'B' and resid 85 through 90 removed outlier: 3.780A pdb=" N GLU B 89 " --> pdb=" O GLN B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 102 No H-bonds generated for 'chain 'B' and resid 100 through 102' Processing helix chain 'B' and resid 112 through 115 Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' 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: 3.893A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 195 through 212 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 269 removed outlier: 4.312A pdb=" N GLN B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 removed outlier: 3.581A pdb=" N LEU B 282 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 311 removed outlier: 3.685A pdb=" N LYS B 311 " --> pdb=" O ARG B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 382 Processing helix chain 'B' and resid 395 through 404 removed outlier: 5.584A pdb=" N THR B 403 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLU B 404 " --> pdb=" O THR B 400 " (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 414 through 416 removed outlier: 6.693A pdb=" N PHE A 389 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 329 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLN A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 464 through 470 removed outlier: 8.491A pdb=" N PHE A 440 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASN A 494 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL A 442 " --> pdb=" O ASN A 494 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL A 496 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N GLY A 444 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYS A 530 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ILE A 495 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TYR A 532 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N THR A 497 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ALA A 534 " --> pdb=" O THR A 497 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 47 through 49 Processing sheet with id= E, first strand: chain 'B' and resid 60 through 63 Processing sheet with id= F, first strand: chain 'B' and resid 105 through 110 Processing sheet with id= G, first strand: chain 'B' and resid 326 through 328 removed outlier: 6.000A pdb=" N LYS B 388 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLU B 413 " --> pdb=" O PHE B 389 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LEU B 391 " --> pdb=" O GLU B 413 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU B 415 " --> pdb=" O LEU B 391 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 329 through 333 removed outlier: 5.847A pdb=" N GLN B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) 235 hydrogen bonds defined for protein. 654 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 2.59 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1342 1.27 - 1.40: 2187 1.40 - 1.54: 5116 1.54 - 1.67: 220 1.67 - 1.81: 25 Bond restraints: 8890 Sorted by residual: bond pdb=" C5 OMC E 2 " pdb=" C6 OMC E 2 " ideal model delta sigma weight residual 1.488 1.346 0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" C2 OMC E 4 " pdb=" N3 OMC E 4 " ideal model delta sigma weight residual 1.491 1.349 0.142 2.00e-02 2.50e+03 5.02e+01 bond pdb=" C2 OMC E 2 " pdb=" N3 OMC E 2 " ideal model delta sigma weight residual 1.491 1.349 0.142 2.00e-02 2.50e+03 5.02e+01 bond pdb=" N3 OMC E 2 " pdb=" C4 OMC E 2 " ideal model delta sigma weight residual 1.448 1.316 0.132 2.00e-02 2.50e+03 4.37e+01 bond pdb=" O3' DC E 3 " pdb=" P OMC E 4 " ideal model delta sigma weight residual 1.607 1.700 -0.093 1.50e-02 4.44e+03 3.81e+01 ... (remaining 8885 not shown) Histogram of bond angle deviations from ideal: 99.92 - 115.93: 6170 115.93 - 131.94: 6019 131.94 - 147.95: 40 147.95 - 163.96: 0 163.96 - 179.97: 2 Bond angle restraints: 12231 Sorted by residual: angle pdb=" C5' DA E 25 " pdb=" C4' DA E 25 " pdb=" O4' DA E 25 " ideal model delta sigma weight residual 109.40 116.92 -7.52 1.50e+00 4.44e-01 2.51e+01 angle pdb=" C2 T27 A 601 " pdb=" C1 T27 A 601 " pdb=" C7 T27 A 601 " ideal model delta sigma weight residual 120.40 105.52 14.88 3.00e+00 1.11e-01 2.46e+01 angle pdb=" C6 T27 A 601 " pdb=" C1 T27 A 601 " pdb=" C7 T27 A 601 " ideal model delta sigma weight residual 121.15 131.96 -10.81 3.00e+00 1.11e-01 1.30e+01 angle pdb=" C3' OMC E 4 " pdb=" C2' OMC E 4 " pdb=" C1' OMC E 4 " ideal model delta sigma weight residual 101.30 104.74 -3.44 1.00e+00 1.00e+00 1.19e+01 angle pdb=" C12 T27 A 601 " pdb=" N4 T27 A 601 " pdb=" C16 T27 A 601 " ideal model delta sigma weight residual 131.80 123.10 8.70 3.00e+00 1.11e-01 8.41e+00 ... (remaining 12226 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 4490 17.84 - 35.68: 570 35.68 - 53.52: 110 53.52 - 71.36: 35 71.36 - 89.20: 10 Dihedral angle restraints: 5215 sinusoidal: 2417 harmonic: 2798 Sorted by residual: dihedral pdb=" CA PRO B 4 " pdb=" CB PRO B 4 " pdb=" CG PRO B 4 " pdb=" CD PRO B 4 " ideal model delta sinusoidal sigma weight residual 38.00 115.32 -77.32 1 2.00e+01 2.50e-03 1.87e+01 dihedral pdb=" CA GLU A 224 " pdb=" C GLU A 224 " pdb=" N PRO A 225 " pdb=" CA PRO A 225 " ideal model delta harmonic sigma weight residual 180.00 160.54 19.46 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA ILE A 309 " pdb=" C ILE A 309 " pdb=" N LEU A 310 " pdb=" CA LEU A 310 " ideal model delta harmonic sigma weight residual -180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 5212 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1183 0.075 - 0.150: 136 0.150 - 0.225: 1 0.225 - 0.300: 0 0.300 - 0.375: 1 Chirality restraints: 1321 Sorted by residual: chirality pdb=" C4' DA E 25 " pdb=" C5' DA E 25 " pdb=" O4' DA E 25 " pdb=" C3' DA E 25 " both_signs ideal model delta sigma weight residual False -2.53 -2.15 -0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" C3' DT E 8 " pdb=" C4' DT E 8 " pdb=" O3' DT E 8 " pdb=" C2' DT E 8 " both_signs ideal model delta sigma weight residual False -2.66 -2.47 -0.19 2.00e-01 2.50e+01 9.34e-01 chirality pdb=" CA ILE B 180 " pdb=" N ILE B 180 " pdb=" C ILE B 180 " pdb=" CB ILE B 180 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 ... (remaining 1318 not shown) Planarity restraints: 1423 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC E 2 " -0.053 2.00e-02 2.50e+03 5.50e-01 6.80e+03 pdb=" C4' OMC E 2 " -0.415 2.00e-02 2.50e+03 pdb=" O4' OMC E 2 " -0.524 2.00e-02 2.50e+03 pdb=" C3' OMC E 2 " 0.590 2.00e-02 2.50e+03 pdb=" O3' OMC E 2 " 0.564 2.00e-02 2.50e+03 pdb=" C2' OMC E 2 " 0.198 2.00e-02 2.50e+03 pdb=" O2' OMC E 2 " -0.923 2.00e-02 2.50e+03 pdb=" C1' OMC E 2 " -0.244 2.00e-02 2.50e+03 pdb=" N1 OMC E 2 " 0.807 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC E 4 " -0.025 2.00e-02 2.50e+03 5.39e-01 6.54e+03 pdb=" C4' OMC E 4 " 0.427 2.00e-02 2.50e+03 pdb=" O4' OMC E 4 " 0.574 2.00e-02 2.50e+03 pdb=" C3' OMC E 4 " -0.600 2.00e-02 2.50e+03 pdb=" O3' OMC E 4 " -0.507 2.00e-02 2.50e+03 pdb=" C2' OMC E 4 " -0.215 2.00e-02 2.50e+03 pdb=" O2' OMC E 4 " 0.870 2.00e-02 2.50e+03 pdb=" C1' OMC E 4 " 0.260 2.00e-02 2.50e+03 pdb=" N1 OMC E 4 " -0.785 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 420 " 0.046 5.00e-02 4.00e+02 6.98e-02 7.79e+00 pdb=" N PRO A 421 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 421 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 421 " 0.034 5.00e-02 4.00e+02 ... (remaining 1420 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 459 2.73 - 3.27: 7992 3.27 - 3.81: 13937 3.81 - 4.36: 16862 4.36 - 4.90: 28437 Nonbonded interactions: 67687 Sorted by model distance: nonbonded pdb=" NH2 ARG B 356 " pdb=" O ALA B 360 " model vdw 2.187 2.520 nonbonded pdb=" OH TYR B 354 " pdb=" OE2 GLU B 378 " model vdw 2.196 2.440 nonbonded pdb=" NZ LYS B 73 " pdb=" OH TYR B 146 " model vdw 2.216 2.520 nonbonded pdb=" NZ LYS B 366 " pdb=" OE2 GLU B 370 " model vdw 2.221 2.520 nonbonded pdb=" OE2 GLU A 328 " pdb=" OH TYR A 342 " model vdw 2.229 2.440 ... (remaining 67682 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 35 5.49 5 S 13 5.16 5 C 5452 2.51 5 N 1432 2.21 5 O 1659 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.180 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: 1.260 Check model and map are aligned: 0.140 Process input model: 27.840 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.142 8890 Z= 0.395 Angle : 0.651 14.883 12231 Z= 0.340 Chirality : 0.044 0.375 1321 Planarity : 0.021 0.550 1423 Dihedral : 16.334 89.196 3411 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.02 (0.28), residues: 951 helix: 1.36 (0.32), residues: 307 sheet: 0.11 (0.42), residues: 157 loop : -0.97 (0.29), residues: 487 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.895 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.2203 time to fit residues: 36.3314 Evaluate side-chains 96 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.848 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 40.0000 chunk 74 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 46 optimal weight: 30.0000 chunk 57 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN B 207 GLN B 367 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.059 8890 Z= 0.423 Angle : 0.807 14.177 12231 Z= 0.455 Chirality : 0.047 0.168 1321 Planarity : 0.008 0.112 1423 Dihedral : 16.064 86.660 1384 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.82 (0.27), residues: 951 helix: 0.52 (0.30), residues: 314 sheet: -0.65 (0.40), residues: 168 loop : -1.20 (0.29), residues: 469 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 0.888 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 113 average time/residue: 0.2221 time to fit residues: 34.7654 Evaluate side-chains 104 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0747 time to fit residues: 2.1680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 chunk 79 optimal weight: 6.9990 chunk 88 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 71 optimal weight: 0.0470 overall best weight: 1.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 500 GLN B 367 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8890 Z= 0.164 Angle : 0.662 13.940 12231 Z= 0.385 Chirality : 0.040 0.162 1321 Planarity : 0.006 0.113 1423 Dihedral : 15.580 81.463 1384 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.26 (0.28), residues: 951 helix: 1.23 (0.31), residues: 306 sheet: -0.51 (0.39), residues: 173 loop : -0.96 (0.29), residues: 472 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 119 time to evaluate : 1.042 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 122 average time/residue: 0.2305 time to fit residues: 39.1261 Evaluate side-chains 106 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 101 time to evaluate : 0.958 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0830 time to fit residues: 2.1278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 46 optimal weight: 30.0000 chunk 9 optimal weight: 10.0000 chunk 42 optimal weight: 0.0970 chunk 59 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 84 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN A 255 ASN B 54 ASN B 367 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 8890 Z= 0.157 Angle : 0.642 13.127 12231 Z= 0.375 Chirality : 0.039 0.138 1321 Planarity : 0.006 0.113 1423 Dihedral : 15.485 87.422 1384 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.01 (0.29), residues: 951 helix: 1.54 (0.32), residues: 306 sheet: -0.22 (0.41), residues: 167 loop : -0.92 (0.29), residues: 478 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 111 time to evaluate : 1.010 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 113 average time/residue: 0.2161 time to fit residues: 34.3403 Evaluate side-chains 105 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 0.909 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0805 time to fit residues: 1.7767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 20.0000 chunk 1 optimal weight: 0.7980 chunk 70 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 48 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN B 54 ASN B 367 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 8890 Z= 0.247 Angle : 0.684 12.547 12231 Z= 0.393 Chirality : 0.042 0.152 1321 Planarity : 0.007 0.117 1423 Dihedral : 15.593 99.338 1384 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.18 (0.28), residues: 951 helix: 1.33 (0.31), residues: 300 sheet: -0.51 (0.40), residues: 174 loop : -0.90 (0.30), residues: 477 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 1.013 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 106 average time/residue: 0.2187 time to fit residues: 32.3089 Evaluate side-chains 102 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 97 time to evaluate : 0.913 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0835 time to fit residues: 2.1430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 55 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN B 367 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8890 Z= 0.192 Angle : 0.659 12.857 12231 Z= 0.380 Chirality : 0.040 0.141 1321 Planarity : 0.006 0.115 1423 Dihedral : 15.501 98.127 1384 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.11 (0.29), residues: 951 helix: 1.40 (0.32), residues: 300 sheet: -0.46 (0.40), residues: 174 loop : -0.86 (0.30), residues: 477 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 103 time to evaluate : 1.032 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 105 average time/residue: 0.2231 time to fit residues: 32.9098 Evaluate side-chains 103 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 0.924 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0876 time to fit residues: 2.0977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 79 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 chunk 94 optimal weight: 0.0070 chunk 59 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 overall best weight: 4.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN B 367 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 8890 Z= 0.262 Angle : 0.694 12.649 12231 Z= 0.398 Chirality : 0.043 0.153 1321 Planarity : 0.007 0.118 1423 Dihedral : 15.576 98.407 1384 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.28), residues: 951 helix: 1.17 (0.31), residues: 300 sheet: -0.89 (0.39), residues: 184 loop : -0.88 (0.30), residues: 467 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 0.903 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 101 average time/residue: 0.2401 time to fit residues: 33.2198 Evaluate side-chains 97 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 0.937 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1087 time to fit residues: 2.0315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 chunk 46 optimal weight: 30.0000 chunk 8 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN B 207 GLN B 367 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 8890 Z= 0.223 Angle : 0.678 12.783 12231 Z= 0.390 Chirality : 0.041 0.149 1321 Planarity : 0.006 0.116 1423 Dihedral : 15.514 97.456 1384 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.34 (0.28), residues: 951 helix: 1.18 (0.31), residues: 300 sheet: -0.77 (0.40), residues: 178 loop : -0.89 (0.30), residues: 473 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 0.915 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 100 average time/residue: 0.2417 time to fit residues: 33.2241 Evaluate side-chains 96 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 1.034 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0852 time to fit residues: 1.5232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 40.0000 chunk 88 optimal weight: 0.4980 chunk 90 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 chunk 38 optimal weight: 0.0370 chunk 69 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 83 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 overall best weight: 3.1064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN B 207 GLN B 367 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8890 Z= 0.209 Angle : 0.668 12.803 12231 Z= 0.385 Chirality : 0.041 0.145 1321 Planarity : 0.006 0.116 1423 Dihedral : 15.451 96.597 1384 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.28 (0.28), residues: 951 helix: 1.23 (0.31), residues: 300 sheet: -0.72 (0.40), residues: 178 loop : -0.86 (0.30), residues: 473 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 1.009 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 106 average time/residue: 0.2321 time to fit residues: 34.0350 Evaluate side-chains 106 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 0.943 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0865 time to fit residues: 2.4776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 44 optimal weight: 30.0000 chunk 64 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 chunk 77 optimal weight: 30.0000 chunk 8 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN B 367 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 8890 Z= 0.291 Angle : 0.716 12.600 12231 Z= 0.407 Chirality : 0.043 0.156 1321 Planarity : 0.007 0.118 1423 Dihedral : 15.630 97.262 1384 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 951 helix: 1.02 (0.31), residues: 298 sheet: -0.89 (0.39), residues: 178 loop : -1.00 (0.29), residues: 475 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 0.979 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 103 average time/residue: 0.2385 time to fit residues: 33.7512 Evaluate side-chains 104 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 0.867 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0821 time to fit residues: 1.8477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 30.0000 chunk 23 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 79 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 367 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.211117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.173456 restraints weight = 9553.171| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 2.12 r_work: 0.3785 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8890 Z= 0.220 Angle : 0.682 12.821 12231 Z= 0.391 Chirality : 0.041 0.147 1321 Planarity : 0.006 0.116 1423 Dihedral : 15.543 96.386 1384 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 951 helix: 1.18 (0.31), residues: 298 sheet: -0.81 (0.40), residues: 178 loop : -0.96 (0.29), residues: 475 =============================================================================== Job complete usr+sys time: 1634.49 seconds wall clock time: 30 minutes 58.02 seconds (1858.02 seconds total)