Starting phenix.real_space_refine on Mon Mar 11 15:33:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2d_14462/03_2024/7z2d_14462_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2d_14462/03_2024/7z2d_14462.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2d_14462/03_2024/7z2d_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_14462/03_2024/7z2d_14462_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2d_14462/03_2024/7z2d_14462_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2d_14462/03_2024/7z2d_14462.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2d_14462/03_2024/7z2d_14462.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2d_14462/03_2024/7z2d_14462_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2d_14462/03_2024/7z2d_14462_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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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. 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-5265/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: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'T27': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.09, per 1000 atoms: 0.59 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: 3.36 Conformation dependent library (CDL) restraints added in 1.5 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: 3.46 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: 2.44 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: 1.13 - 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: 4495 17.84 - 35.68: 573 35.68 - 53.52: 112 53.52 - 71.36: 38 71.36 - 89.20: 10 Dihedral angle restraints: 5228 sinusoidal: 2430 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 5225 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 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: 0.110 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: 0.980 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.500 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 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 : 16.447 89.196 3424 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 % Allowed : 0.23 % Favored : 99.77 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 402 HIS 0.006 0.001 HIS B 208 PHE 0.010 0.001 PHE B 130 TYR 0.013 0.001 TYR A 319 ARG 0.002 0.000 ARG A 83 *********************** 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: 0.2116 time to fit residues: 35.0478 Evaluate side-chains 96 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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: 0.6924 moved from start: 0.1367 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= 0.419 Angle : 0.806 14.381 12231 Z= 0.453 Chirality : 0.047 0.188 1321 Planarity : 0.008 0.113 1423 Dihedral : 16.163 86.531 1397 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 1.40 % Allowed : 9.08 % Favored : 89.52 % 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: -0.80 (0.27), residues: 951 helix: 0.53 (0.30), residues: 314 sheet: -0.64 (0.40), residues: 168 loop : -1.20 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 402 HIS 0.006 0.002 HIS B 361 PHE 0.015 0.002 PHE B 130 TYR 0.025 0.003 TYR B 144 ARG 0.004 0.001 ARG B 143 *********************** 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 118 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 0.992 Fit side-chains REVERT: A 47 ILE cc_start: 0.7485 (mm) cc_final: 0.7018 (mt) outliers start: 12 outliers final: 7 residues processed: 113 average time/residue: 0.2231 time to fit residues: 34.7388 Evaluate side-chains 105 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 286 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 30 optimal weight: 0.0870 chunk 71 optimal weight: 0.9980 overall best weight: 2.0162 ------------------------------------------------------------------------------- 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: 0.6826 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8890 Z= 0.183 Angle : 0.672 13.950 12231 Z= 0.390 Chirality : 0.041 0.142 1321 Planarity : 0.007 0.113 1423 Dihedral : 15.735 82.818 1397 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.28 % Allowed : 11.06 % Favored : 87.66 % 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: 1.07 (0.31), residues: 308 sheet: -0.47 (0.40), residues: 167 loop : -1.05 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 402 HIS 0.006 0.001 HIS B 208 PHE 0.006 0.001 PHE B 130 TYR 0.014 0.001 TYR A 144 ARG 0.002 0.000 ARG A 83 *********************** 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 126 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 0.947 Fit side-chains REVERT: A 47 ILE cc_start: 0.7420 (mm) cc_final: 0.6968 (mt) outliers start: 11 outliers final: 9 residues processed: 119 average time/residue: 0.2229 time to fit residues: 36.6781 Evaluate side-chains 111 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 20.0000 chunk 67 optimal weight: 7.9990 chunk 46 optimal weight: 30.0000 chunk 9 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 367 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.1331 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 : 0.680 13.074 12231 Z= 0.392 Chirality : 0.041 0.147 1321 Planarity : 0.007 0.116 1423 Dihedral : 15.829 87.436 1397 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.75 % Allowed : 13.04 % Favored : 85.22 % 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: -0.42 (0.28), residues: 951 helix: 1.08 (0.31), residues: 308 sheet: -0.57 (0.40), residues: 168 loop : -1.06 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 402 HIS 0.004 0.001 HIS B 208 PHE 0.008 0.001 PHE B 130 TYR 0.017 0.001 TYR B 144 ARG 0.002 0.000 ARG A 358 *********************** 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 126 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 0.996 Fit side-chains REVERT: A 47 ILE cc_start: 0.7453 (mm) cc_final: 0.7008 (mt) outliers start: 15 outliers final: 12 residues processed: 118 average time/residue: 0.2079 time to fit residues: 34.1174 Evaluate side-chains 114 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 48 optimal weight: 20.0000 chunk 85 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8890 Z= 0.317 Angle : 0.731 12.700 12231 Z= 0.417 Chirality : 0.044 0.162 1321 Planarity : 0.007 0.118 1423 Dihedral : 15.957 101.798 1397 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 2.21 % Allowed : 15.48 % Favored : 82.31 % 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: -0.72 (0.28), residues: 951 helix: 0.79 (0.31), residues: 306 sheet: -0.98 (0.39), residues: 176 loop : -1.09 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 402 HIS 0.005 0.001 HIS B 361 PHE 0.012 0.002 PHE B 130 TYR 0.021 0.002 TYR B 144 ARG 0.003 0.000 ARG A 358 *********************** 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 124 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 105 time to evaluate : 0.996 Fit side-chains REVERT: A 47 ILE cc_start: 0.7439 (mm) cc_final: 0.7023 (mt) outliers start: 19 outliers final: 18 residues processed: 119 average time/residue: 0.2113 time to fit residues: 34.8431 Evaluate side-chains 113 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 94 optimal weight: 20.0000 chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8890 Z= 0.273 Angle : 0.708 12.784 12231 Z= 0.405 Chirality : 0.043 0.155 1321 Planarity : 0.007 0.117 1423 Dihedral : 15.955 100.043 1397 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.10 % Allowed : 17.35 % Favored : 80.56 % 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: -0.72 (0.28), residues: 951 helix: 0.92 (0.31), residues: 299 sheet: -1.08 (0.39), residues: 178 loop : -1.12 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 402 HIS 0.004 0.001 HIS B 361 PHE 0.012 0.002 PHE A 227 TYR 0.018 0.002 TYR B 144 ARG 0.002 0.000 ARG A 358 *********************** 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 119 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 1.004 Fit side-chains REVERT: A 47 ILE cc_start: 0.7403 (mm) cc_final: 0.7002 (mt) outliers start: 18 outliers final: 17 residues processed: 112 average time/residue: 0.2135 time to fit residues: 33.1035 Evaluate side-chains 113 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 GLN B 367 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8890 Z= 0.274 Angle : 0.707 12.752 12231 Z= 0.404 Chirality : 0.043 0.158 1321 Planarity : 0.007 0.118 1423 Dihedral : 16.020 99.838 1397 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.33 % Allowed : 17.58 % Favored : 80.09 % 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: -0.77 (0.28), residues: 951 helix: 0.88 (0.31), residues: 301 sheet: -1.09 (0.39), residues: 178 loop : -1.17 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 402 HIS 0.004 0.001 HIS B 361 PHE 0.010 0.002 PHE A 227 TYR 0.019 0.002 TYR B 144 ARG 0.002 0.000 ARG A 358 *********************** 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 122 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 0.907 Fit side-chains REVERT: A 47 ILE cc_start: 0.7412 (mm) cc_final: 0.7016 (mt) REVERT: B 181 TYR cc_start: 0.7408 (t80) cc_final: 0.7117 (t80) outliers start: 20 outliers final: 19 residues processed: 114 average time/residue: 0.2091 time to fit residues: 33.4009 Evaluate side-chains 115 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 28 optimal weight: 20.0000 chunk 18 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 85 optimal weight: 0.0570 chunk 90 optimal weight: 0.7980 overall best weight: 1.4902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 GLN B 367 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.1583 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= 0.165 Angle : 0.658 13.093 12231 Z= 0.381 Chirality : 0.040 0.144 1321 Planarity : 0.006 0.114 1423 Dihedral : 15.789 97.909 1397 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.75 % Allowed : 18.28 % Favored : 79.98 % 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: -0.33 (0.28), residues: 951 helix: 1.33 (0.32), residues: 299 sheet: -0.89 (0.39), residues: 177 loop : -0.94 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 402 HIS 0.004 0.001 HIS B 208 PHE 0.007 0.001 PHE A 227 TYR 0.014 0.001 TYR A 144 ARG 0.001 0.000 ARG A 125 *********************** 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 123 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 1.009 Fit side-chains REVERT: A 47 ILE cc_start: 0.7468 (mm) cc_final: 0.7035 (mt) REVERT: B 181 TYR cc_start: 0.7351 (t80) cc_final: 0.7086 (t80) outliers start: 15 outliers final: 14 residues processed: 115 average time/residue: 0.2202 time to fit residues: 35.3750 Evaluate side-chains 111 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 423 VAL 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: 6.9990 chunk 90 optimal weight: 0.0470 chunk 52 optimal weight: 9.9990 chunk 38 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 79 optimal weight: 0.0170 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 overall best weight: 0.8118 ------------------------------------------------------------------------------- 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 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8890 Z= 0.152 Angle : 0.648 12.996 12231 Z= 0.374 Chirality : 0.039 0.141 1321 Planarity : 0.006 0.113 1423 Dihedral : 15.436 95.892 1397 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.05 % Allowed : 18.74 % Favored : 80.21 % 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: 0.04 (0.29), residues: 951 helix: 1.65 (0.32), residues: 299 sheet: -0.32 (0.41), residues: 169 loop : -0.88 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 402 HIS 0.005 0.000 HIS B 208 PHE 0.012 0.001 PHE B 77 TYR 0.014 0.001 TYR A 319 ARG 0.003 0.000 ARG B 356 *********************** 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 113 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 47 ILE cc_start: 0.7438 (mm) cc_final: 0.6985 (mt) REVERT: A 115 TYR cc_start: 0.7405 (t80) cc_final: 0.6663 (t80) REVERT: A 516 GLU cc_start: 0.6598 (tp30) cc_final: 0.5528 (pm20) REVERT: B 181 TYR cc_start: 0.7324 (t80) cc_final: 0.7076 (t80) outliers start: 9 outliers final: 9 residues processed: 109 average time/residue: 0.1967 time to fit residues: 30.0357 Evaluate side-chains 105 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 10.0000 chunk 56 optimal weight: 0.0670 chunk 44 optimal weight: 30.0000 chunk 64 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 8 optimal weight: 0.0570 chunk 60 optimal weight: 5.9990 chunk 47 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 overall best weight: 2.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 207 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.1602 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= 0.193 Angle : 0.667 12.722 12231 Z= 0.381 Chirality : 0.041 0.320 1321 Planarity : 0.006 0.116 1423 Dihedral : 15.477 96.010 1397 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.40 % Allowed : 18.51 % Favored : 80.09 % 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 (0.28), residues: 951 helix: 1.46 (0.32), residues: 299 sheet: -0.63 (0.40), residues: 178 loop : -0.82 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 402 HIS 0.005 0.001 HIS B 208 PHE 0.008 0.001 PHE A 227 TYR 0.013 0.001 TYR B 144 ARG 0.001 0.000 ARG B 78 ********************** 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 107 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.874 Fit side-chains REVERT: A 47 ILE cc_start: 0.7490 (mm) cc_final: 0.7016 (mt) REVERT: A 516 GLU cc_start: 0.6750 (tp30) cc_final: 0.5543 (pm20) REVERT: B 181 TYR cc_start: 0.7303 (t80) cc_final: 0.7051 (t80) outliers start: 12 outliers final: 11 residues processed: 103 average time/residue: 0.2147 time to fit residues: 30.8205 Evaluate side-chains 103 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 40.0000 chunk 23 optimal weight: 3.9990 chunk 71 optimal weight: 20.0000 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 79 optimal weight: 20.0000 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 207 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.210027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.171541 restraints weight = 9515.798| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.17 r_work: 0.3724 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.1628 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= 0.181 Angle : 0.662 12.816 12231 Z= 0.379 Chirality : 0.041 0.309 1321 Planarity : 0.006 0.115 1423 Dihedral : 15.435 95.078 1397 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.28 % Allowed : 18.74 % Favored : 79.98 % 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: -0.09 (0.28), residues: 951 helix: 1.46 (0.32), residues: 298 sheet: -0.58 (0.40), residues: 177 loop : -0.80 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 402 HIS 0.004 0.001 HIS B 208 PHE 0.006 0.001 PHE B 77 TYR 0.012 0.001 TYR A 144 ARG 0.001 0.000 ARG B 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1767.13 seconds wall clock time: 33 minutes 10.00 seconds (1990.00 seconds total)