Starting phenix.real_space_refine on Wed Feb 14 02:21:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2h_14466/02_2024/7z2h_14466_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2h_14466/02_2024/7z2h_14466.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2h_14466/02_2024/7z2h_14466_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2h_14466/02_2024/7z2h_14466_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2h_14466/02_2024/7z2h_14466_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2h_14466/02_2024/7z2h_14466.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2h_14466/02_2024/7z2h_14466.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2h_14466/02_2024/7z2h_14466_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2h_14466/02_2024/7z2h_14466_updated.pdb" } resolution = 3.58 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= 0.001 sd= 0.017 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: 7 Type Number sf(0) Gaussians P 36 5.49 5 S 13 5.16 5 Cl 1 4.86 5 C 5333 2.51 5 N 1405 2.21 5 O 1623 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 72": "NH1" <-> "NH2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 328": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8414 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4254 Classifications: {'peptide': 526} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 489} Chain breaks: 5 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3390 Classifications: {'peptide': 411} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 741 Classifications: {'DNA': 34, 'RNA': 2} Modifications used: {'rna3p': 2} Link IDs: {'rna3p': 35} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'2KW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.90, per 1000 atoms: 0.58 Number of scatterers: 8414 At special positions: 0 Unit cell: (97, 110.58, 96.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 13 16.00 P 36 15.00 F 3 9.00 O 1623 8.00 N 1405 7.00 C 5333 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: 3.49 Conformation dependent library (CDL) restraints added in 1.4 seconds 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1766 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 10 sheets defined 35.0% alpha, 10.4% beta 13 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 3.61 Creating SS restraints... Processing helix chain 'A' and resid 36 through 44 removed outlier: 3.558A pdb=" N GLU A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N MET A 41 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU A 42 " --> pdb=" O CYS A 38 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS A 43 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 36 through 44' Processing helix chain 'A' and resid 80 through 83 No H-bonds generated for 'chain 'A' and resid 80 through 83' Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.790A pdb=" N LYS A 126 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 174 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 195 through 212 removed outlier: 3.934A pdb=" N TRP A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 254 through 269 removed outlier: 4.252A pdb=" N GLN A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 285 removed outlier: 4.510A pdb=" N LEU A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLY A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 311 Processing helix chain 'A' and resid 364 through 383 Processing helix chain 'A' and resid 395 through 404 Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 500 through 508 removed outlier: 3.968A pdb=" N ALA A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 527 Processing helix chain 'A' and resid 543 through 551 removed outlier: 4.252A pdb=" N GLU A 546 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN A 547 " --> pdb=" O GLY A 544 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL A 548 " --> pdb=" O ASN A 545 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP A 549 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU A 551 " --> pdb=" O VAL A 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 43 removed outlier: 3.747A pdb=" N GLU B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 90 removed outlier: 6.508A pdb=" N ASP B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TRP B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 112 through 117 Processing helix chain 'B' and resid 124 through 127 Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 154 through 174 removed outlier: 4.288A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 195 through 212 removed outlier: 3.520A pdb=" N THR B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TRP B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 254 through 270 removed outlier: 3.783A pdb=" N GLN B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE B 270 " --> pdb=" O TRP B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 Processing helix chain 'B' and resid 297 through 311 Processing helix chain 'B' and resid 365 through 382 Processing helix chain 'B' and resid 395 through 405 removed outlier: 3.770A pdb=" N TRP B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N THR B 403 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLU B 404 " --> pdb=" O THR B 400 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR B 405 " --> pdb=" O TRP B 401 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 47 through 50 removed outlier: 4.014A pdb=" N ARG A 143 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 105 through 107 Processing sheet with id= C, first strand: chain 'A' and resid 232 through 234 Processing sheet with id= D, first strand: chain 'A' and resid 328 through 331 removed outlier: 3.759A pdb=" N GLU A 328 " --> pdb=" O GLN A 340 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 389 through 391 Processing sheet with id= F, first strand: chain 'A' and resid 438 through 441 removed outlier: 4.193A pdb=" N GLU A 438 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LYS A 530 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ILE A 495 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TYR A 532 " --> pdb=" O ILE A 495 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 453 through 455 Processing sheet with id= H, first strand: chain 'B' and resid 47 through 49 removed outlier: 3.768A pdb=" N ILE B 142 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE B 132 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 105 through 110 Processing sheet with id= J, first strand: chain 'B' and resid 348 through 355 removed outlier: 6.731A pdb=" N ILE B 341 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N THR B 351 " --> pdb=" O TYR B 339 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TYR B 339 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS B 353 " --> pdb=" O TRP B 337 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP B 337 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 391 " --> pdb=" O GLU B 415 " (cutoff:3.500A) 235 hydrogen bonds defined for protein. 660 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 2.49 Time building geometry restraints manager: 3.73 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: 1304 1.27 - 1.40: 2156 1.40 - 1.54: 5045 1.54 - 1.67: 181 1.67 - 1.81: 24 Bond restraints: 8710 Sorted by residual: bond pdb=" C10 2KW A 601 " pdb=" C9 2KW A 601 " ideal model delta sigma weight residual 1.354 1.522 -0.168 2.00e-02 2.50e+03 7.08e+01 bond pdb=" C21 2KW A 601 " pdb=" N20 2KW A 601 " ideal model delta sigma weight residual 1.356 1.500 -0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" C2 OMC E 2 " pdb=" N3 OMC E 2 " ideal model delta sigma weight residual 1.491 1.350 0.141 2.00e-02 2.50e+03 5.00e+01 bond pdb=" C2 OMC E 4 " pdb=" N3 OMC E 4 " ideal model delta sigma weight residual 1.491 1.352 0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C10 2KW A 601 " pdb=" N11 2KW A 601 " ideal model delta sigma weight residual 1.355 1.489 -0.134 2.00e-02 2.50e+03 4.50e+01 ... (remaining 8705 not shown) Histogram of bond angle deviations from ideal: 94.12 - 111.29: 4018 111.29 - 128.46: 7839 128.46 - 145.63: 139 145.63 - 162.80: 0 162.80 - 179.97: 1 Bond angle restraints: 11997 Sorted by residual: angle pdb=" C LEU A 228 " pdb=" CA LEU A 228 " pdb=" CB LEU A 228 " ideal model delta sigma weight residual 110.24 122.50 -12.26 1.46e+00 4.69e-01 7.05e+01 angle pdb=" N LEU A 228 " pdb=" CA LEU A 228 " pdb=" C LEU A 228 " ideal model delta sigma weight residual 108.13 94.42 13.71 1.72e+00 3.38e-01 6.35e+01 angle pdb=" C ASP A 186 " pdb=" CA ASP A 186 " pdb=" CB ASP A 186 " ideal model delta sigma weight residual 109.33 94.12 15.21 1.97e+00 2.58e-01 5.96e+01 angle pdb=" N TRP B 426 " pdb=" CA TRP B 426 " pdb=" C TRP B 426 " ideal model delta sigma weight residual 112.89 105.54 7.35 1.24e+00 6.50e-01 3.51e+01 angle pdb=" N ILE B 382 " pdb=" CA ILE B 382 " pdb=" C ILE B 382 " ideal model delta sigma weight residual 110.74 116.07 -5.33 9.10e-01 1.21e+00 3.44e+01 ... (remaining 11992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 4349 17.77 - 35.55: 535 35.55 - 53.32: 174 53.32 - 71.10: 51 71.10 - 88.87: 12 Dihedral angle restraints: 5121 sinusoidal: 2387 harmonic: 2734 Sorted by residual: dihedral pdb=" C ASP A 186 " pdb=" N ASP A 186 " pdb=" CA ASP A 186 " pdb=" CB ASP A 186 " ideal model delta harmonic sigma weight residual -122.60 -105.98 -16.62 0 2.50e+00 1.60e-01 4.42e+01 dihedral pdb=" C MET A 164 " pdb=" N MET A 164 " pdb=" CA MET A 164 " pdb=" CB MET A 164 " ideal model delta harmonic sigma weight residual -122.60 -135.65 13.05 0 2.50e+00 1.60e-01 2.73e+01 dihedral pdb=" N MET A 164 " pdb=" C MET A 164 " pdb=" CA MET A 164 " pdb=" CB MET A 164 " ideal model delta harmonic sigma weight residual 122.80 134.93 -12.13 0 2.50e+00 1.60e-01 2.35e+01 ... (remaining 5118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 1273 0.123 - 0.246: 24 0.246 - 0.369: 3 0.369 - 0.492: 0 0.492 - 0.616: 2 Chirality restraints: 1302 Sorted by residual: chirality pdb=" P DA E -2 " pdb=" OP1 DA E -2 " pdb=" OP2 DA E -2 " pdb=" O5' DA E -2 " both_signs ideal model delta sigma weight residual True 2.35 -2.96 -0.62 2.00e-01 2.50e+01 9.47e+00 chirality pdb=" CA MET A 164 " pdb=" N MET A 164 " pdb=" C MET A 164 " pdb=" CB MET A 164 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.53 2.00e-01 2.50e+01 6.90e+00 chirality pdb=" C4' DC E 3 " pdb=" C5' DC E 3 " pdb=" O4' DC E 3 " pdb=" C3' DC E 3 " both_signs ideal model delta sigma weight residual False -2.53 -2.80 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 1299 not shown) Planarity restraints: 1384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC E 2 " 0.286 2.00e-02 2.50e+03 4.50e-01 4.55e+03 pdb=" C4' OMC E 2 " -0.403 2.00e-02 2.50e+03 pdb=" O4' OMC E 2 " -0.735 2.00e-02 2.50e+03 pdb=" C3' OMC E 2 " 0.489 2.00e-02 2.50e+03 pdb=" O3' OMC E 2 " 0.085 2.00e-02 2.50e+03 pdb=" C2' OMC E 2 " 0.368 2.00e-02 2.50e+03 pdb=" O2' OMC E 2 " -0.394 2.00e-02 2.50e+03 pdb=" C1' OMC E 2 " -0.325 2.00e-02 2.50e+03 pdb=" N1 OMC E 2 " 0.628 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC E 4 " -0.336 2.00e-02 2.50e+03 4.08e-01 3.75e+03 pdb=" C4' OMC E 4 " 0.375 2.00e-02 2.50e+03 pdb=" O4' OMC E 4 " 0.644 2.00e-02 2.50e+03 pdb=" C3' OMC E 4 " -0.464 2.00e-02 2.50e+03 pdb=" O3' OMC E 4 " 0.047 2.00e-02 2.50e+03 pdb=" C2' OMC E 4 " -0.389 2.00e-02 2.50e+03 pdb=" O2' OMC E 4 " 0.282 2.00e-02 2.50e+03 pdb=" C1' OMC E 4 " 0.350 2.00e-02 2.50e+03 pdb=" N1 OMC E 4 " -0.510 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 125 " -0.565 9.50e-02 1.11e+02 2.53e-01 3.93e+01 pdb=" NE ARG A 125 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG A 125 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 125 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 125 " -0.019 2.00e-02 2.50e+03 ... (remaining 1381 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2011 2.80 - 3.32: 7768 3.32 - 3.85: 14230 3.85 - 4.37: 16303 4.37 - 4.90: 26630 Nonbonded interactions: 66942 Sorted by model distance: nonbonded pdb=" O GLY B 196 " pdb=" OG1 THR B 200 " model vdw 2.274 2.440 nonbonded pdb=" O 2KW A 601 " pdb=" F15 2KW A 601 " model vdw 2.293 2.390 nonbonded pdb=" O ARG A 277 " pdb=" N SER A 280 " model vdw 2.326 2.520 nonbonded pdb=" OG1 THR A 376 " pdb=" OG1 THR A 386 " model vdw 2.344 2.440 nonbonded pdb=" NZ LYS A 13 " pdb=" O LYS A 82 " model vdw 2.377 2.520 ... (remaining 66937 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.070 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: 0.990 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.330 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5965 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 : 0.008 0.168 8710 Z= 0.462 Angle : 0.799 15.210 11997 Z= 0.461 Chirality : 0.054 0.616 1302 Planarity : 0.019 0.450 1384 Dihedral : 17.902 88.870 3355 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.34 % Favored : 95.55 % Rotamer: Outliers : 0.72 % Allowed : 0.84 % Favored : 98.44 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 3.03 % 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: -0.71 (0.28), residues: 921 helix: 0.86 (0.31), residues: 308 sheet: -1.63 (0.42), residues: 149 loop : -0.94 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 414 HIS 0.003 0.001 HIS B 208 PHE 0.012 0.001 PHE A 124 TYR 0.027 0.001 TYR A 232 ARG 0.003 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 144 TYR cc_start: 0.7794 (m-10) cc_final: 0.7447 (m-10) REVERT: B 180 ILE cc_start: 0.7335 (mm) cc_final: 0.6877 (tt) REVERT: B 198 HIS cc_start: 0.4680 (t70) cc_final: 0.4389 (t70) REVERT: B 409 THR cc_start: 0.7210 (m) cc_final: 0.6812 (p) outliers start: 6 outliers final: 2 residues processed: 133 average time/residue: 0.1987 time to fit residues: 36.6735 Evaluate side-chains 108 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain B residue 32 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 30.0000 chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 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 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN B 255 ASN ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6017 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8710 Z= 0.220 Angle : 0.734 14.280 11997 Z= 0.419 Chirality : 0.043 0.183 1302 Planarity : 0.006 0.114 1384 Dihedral : 17.483 113.249 1404 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.34 % Favored : 95.44 % Rotamer: Outliers : 0.72 % Allowed : 7.78 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.53 (0.28), residues: 921 helix: 1.09 (0.31), residues: 302 sheet: -1.49 (0.43), residues: 142 loop : -0.89 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 402 HIS 0.003 0.001 HIS A 315 PHE 0.012 0.002 PHE A 124 TYR 0.015 0.001 TYR A 501 ARG 0.002 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: A 277 ARG cc_start: 0.5978 (mmm160) cc_final: 0.5717 (tpt-90) REVERT: B 180 ILE cc_start: 0.7300 (mm) cc_final: 0.6878 (tt) REVERT: B 198 HIS cc_start: 0.4670 (t70) cc_final: 0.4366 (t70) REVERT: B 409 THR cc_start: 0.7150 (m) cc_final: 0.6783 (p) outliers start: 6 outliers final: 5 residues processed: 116 average time/residue: 0.1875 time to fit residues: 31.8040 Evaluate side-chains 106 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 101 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 137 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 72 optimal weight: 30.0000 chunk 59 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 70 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN A 361 HIS ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6060 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8710 Z= 0.227 Angle : 0.709 13.284 11997 Z= 0.408 Chirality : 0.042 0.174 1302 Planarity : 0.006 0.115 1384 Dihedral : 17.151 107.705 1404 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.32 % Favored : 94.57 % Rotamer: Outliers : 2.16 % Allowed : 11.26 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 921 helix: 1.24 (0.31), residues: 289 sheet: -1.45 (0.42), residues: 148 loop : -0.80 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 398 HIS 0.004 0.001 HIS A 315 PHE 0.013 0.002 PHE B 130 TYR 0.013 0.002 TYR A 457 ARG 0.005 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 MET cc_start: 0.5838 (ttt) cc_final: 0.5413 (tpp) REVERT: A 372 VAL cc_start: 0.5801 (OUTLIER) cc_final: 0.5597 (p) REVERT: B 63 ILE cc_start: 0.8347 (pt) cc_final: 0.8132 (pt) REVERT: B 180 ILE cc_start: 0.7377 (mm) cc_final: 0.6938 (tt) REVERT: B 198 HIS cc_start: 0.4671 (t70) cc_final: 0.4424 (t70) outliers start: 18 outliers final: 13 residues processed: 126 average time/residue: 0.1716 time to fit residues: 31.7243 Evaluate side-chains 113 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 314 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 58 optimal weight: 0.0980 chunk 87 optimal weight: 4.9990 chunk 92 optimal weight: 20.0000 chunk 83 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6070 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8710 Z= 0.226 Angle : 0.713 13.167 11997 Z= 0.410 Chirality : 0.042 0.171 1302 Planarity : 0.006 0.115 1384 Dihedral : 17.058 107.481 1404 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.78 % Favored : 95.11 % Rotamer: Outliers : 2.51 % Allowed : 12.22 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.28), residues: 921 helix: 1.22 (0.31), residues: 290 sheet: -1.50 (0.42), residues: 148 loop : -0.83 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 402 HIS 0.003 0.001 HIS A 315 PHE 0.013 0.002 PHE B 130 TYR 0.018 0.002 TYR A 501 ARG 0.005 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.4632 (mpp) cc_final: 0.4381 (mpp) REVERT: A 357 MET cc_start: 0.5788 (ttt) cc_final: 0.5446 (tpp) REVERT: B 174 GLN cc_start: 0.6424 (mp10) cc_final: 0.6114 (mp10) REVERT: B 180 ILE cc_start: 0.7371 (mm) cc_final: 0.6945 (tt) REVERT: B 198 HIS cc_start: 0.4693 (t70) cc_final: 0.4439 (t70) outliers start: 21 outliers final: 16 residues processed: 122 average time/residue: 0.1676 time to fit residues: 30.4461 Evaluate side-chains 114 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 64 optimal weight: 0.0040 chunk 0 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 overall best weight: 3.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6082 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8710 Z= 0.230 Angle : 0.713 12.988 11997 Z= 0.410 Chirality : 0.042 0.172 1302 Planarity : 0.006 0.115 1384 Dihedral : 16.972 106.232 1404 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.99 % Favored : 94.90 % Rotamer: Outliers : 2.51 % Allowed : 14.49 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.56 (0.28), residues: 921 helix: 1.10 (0.31), residues: 291 sheet: -1.53 (0.41), residues: 149 loop : -0.87 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 402 HIS 0.004 0.001 HIS A 315 PHE 0.014 0.002 PHE B 130 TYR 0.016 0.002 TYR A 501 ARG 0.005 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 MET cc_start: 0.5668 (ttt) cc_final: 0.5366 (tpp) REVERT: A 501 TYR cc_start: 0.5941 (t80) cc_final: 0.5305 (t80) REVERT: B 174 GLN cc_start: 0.6444 (mp10) cc_final: 0.5790 (mp10) REVERT: B 180 ILE cc_start: 0.7413 (mm) cc_final: 0.7013 (tt) REVERT: B 198 HIS cc_start: 0.4783 (t70) cc_final: 0.4519 (t70) outliers start: 21 outliers final: 17 residues processed: 123 average time/residue: 0.1701 time to fit residues: 30.8777 Evaluate side-chains 121 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 30 optimal weight: 0.2980 chunk 48 optimal weight: 0.0270 chunk 89 optimal weight: 0.9990 overall best weight: 1.2442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6012 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 : 0.003 0.032 8710 Z= 0.160 Angle : 0.666 13.017 11997 Z= 0.390 Chirality : 0.040 0.142 1302 Planarity : 0.006 0.113 1384 Dihedral : 16.683 106.196 1404 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.37 % Favored : 96.53 % Rotamer: Outliers : 2.04 % Allowed : 15.81 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.17 (0.28), residues: 921 helix: 1.43 (0.31), residues: 290 sheet: -1.23 (0.43), residues: 148 loop : -0.66 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP B 402 HIS 0.001 0.001 HIS A 208 PHE 0.008 0.001 PHE B 130 TYR 0.015 0.001 TYR A 501 ARG 0.002 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 MET cc_start: 0.5589 (ttt) cc_final: 0.5340 (tpp) REVERT: A 372 VAL cc_start: 0.5750 (p) cc_final: 0.5425 (p) REVERT: A 501 TYR cc_start: 0.5921 (t80) cc_final: 0.5487 (t80) REVERT: B 122 GLU cc_start: 0.5886 (tm-30) cc_final: 0.5561 (tm-30) REVERT: B 174 GLN cc_start: 0.6415 (OUTLIER) cc_final: 0.5863 (mp10) REVERT: B 180 ILE cc_start: 0.7439 (mm) cc_final: 0.7063 (tt) REVERT: B 198 HIS cc_start: 0.4651 (t70) cc_final: 0.4375 (t70) REVERT: B 325 LEU cc_start: 0.6063 (mt) cc_final: 0.5863 (mt) REVERT: B 415 GLU cc_start: 0.6556 (pt0) cc_final: 0.6145 (tp30) outliers start: 17 outliers final: 11 residues processed: 131 average time/residue: 0.1821 time to fit residues: 34.2545 Evaluate side-chains 117 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 174 GLN Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 30.0000 chunk 52 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 92 optimal weight: 0.0270 chunk 57 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 42 optimal weight: 40.0000 chunk 36 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 overall best weight: 2.9244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN B 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6048 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8710 Z= 0.197 Angle : 0.694 12.890 11997 Z= 0.399 Chirality : 0.041 0.169 1302 Planarity : 0.006 0.115 1384 Dihedral : 16.640 104.904 1400 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.67 % Favored : 95.22 % Rotamer: Outliers : 2.63 % Allowed : 16.53 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 921 helix: 1.33 (0.31), residues: 292 sheet: -1.27 (0.43), residues: 149 loop : -0.71 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 402 HIS 0.003 0.001 HIS A 315 PHE 0.013 0.001 PHE B 130 TYR 0.013 0.001 TYR A 501 ARG 0.004 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 2.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 282 LEU cc_start: 0.6179 (OUTLIER) cc_final: 0.5890 (mt) REVERT: A 357 MET cc_start: 0.5599 (ttt) cc_final: 0.5344 (tpp) REVERT: A 501 TYR cc_start: 0.6114 (t80) cc_final: 0.5499 (t80) REVERT: B 122 GLU cc_start: 0.5995 (tm-30) cc_final: 0.5704 (tm-30) REVERT: B 174 GLN cc_start: 0.6434 (OUTLIER) cc_final: 0.5820 (mp10) REVERT: B 180 ILE cc_start: 0.7459 (mm) cc_final: 0.6968 (tt) REVERT: B 198 HIS cc_start: 0.4595 (t70) cc_final: 0.4388 (t70) outliers start: 22 outliers final: 18 residues processed: 120 average time/residue: 0.2193 time to fit residues: 38.9673 Evaluate side-chains 122 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 174 GLN Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 58 optimal weight: 0.0060 chunk 63 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 72 optimal weight: 30.0000 chunk 84 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 overall best weight: 3.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN B 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6057 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8710 Z= 0.204 Angle : 0.697 12.847 11997 Z= 0.401 Chirality : 0.042 0.160 1302 Planarity : 0.006 0.115 1384 Dihedral : 16.638 104.453 1400 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.67 % Favored : 95.22 % Rotamer: Outliers : 2.75 % Allowed : 16.89 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.32 (0.28), residues: 921 helix: 1.31 (0.31), residues: 291 sheet: -1.29 (0.43), residues: 149 loop : -0.77 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 402 HIS 0.003 0.001 HIS A 315 PHE 0.013 0.002 PHE B 130 TYR 0.013 0.001 TYR B 271 ARG 0.004 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 106 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7207 (tt) REVERT: A 282 LEU cc_start: 0.6200 (OUTLIER) cc_final: 0.5909 (mt) REVERT: A 357 MET cc_start: 0.5614 (ttt) cc_final: 0.5339 (tpp) REVERT: A 501 TYR cc_start: 0.6036 (t80) cc_final: 0.5424 (t80) REVERT: B 122 GLU cc_start: 0.5988 (tm-30) cc_final: 0.5730 (tm-30) REVERT: B 174 GLN cc_start: 0.6361 (OUTLIER) cc_final: 0.5721 (mp10) REVERT: B 180 ILE cc_start: 0.7402 (mm) cc_final: 0.7039 (tt) REVERT: B 198 HIS cc_start: 0.4778 (t70) cc_final: 0.4572 (t70) REVERT: B 415 GLU cc_start: 0.6619 (pt0) cc_final: 0.6181 (tp30) outliers start: 23 outliers final: 18 residues processed: 125 average time/residue: 0.1798 time to fit residues: 32.5192 Evaluate side-chains 125 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 104 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 174 GLN Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 51 optimal weight: 0.0980 chunk 37 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 77 optimal weight: 0.0980 chunk 81 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6043 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8710 Z= 0.184 Angle : 0.684 12.875 11997 Z= 0.395 Chirality : 0.041 0.152 1302 Planarity : 0.006 0.115 1384 Dihedral : 16.533 104.025 1400 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.34 % Favored : 95.55 % Rotamer: Outliers : 2.51 % Allowed : 17.25 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.23 (0.28), residues: 921 helix: 1.38 (0.31), residues: 290 sheet: -1.22 (0.43), residues: 149 loop : -0.71 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 402 HIS 0.003 0.001 HIS A 315 PHE 0.011 0.001 PHE B 130 TYR 0.013 0.001 TYR A 501 ARG 0.003 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7161 (tt) REVERT: A 357 MET cc_start: 0.5516 (ttt) cc_final: 0.5280 (tpp) REVERT: A 480 GLN cc_start: 0.5767 (tt0) cc_final: 0.5379 (tt0) REVERT: B 122 GLU cc_start: 0.5998 (tm-30) cc_final: 0.5752 (tm-30) REVERT: B 174 GLN cc_start: 0.6422 (OUTLIER) cc_final: 0.5818 (mp10) REVERT: B 180 ILE cc_start: 0.7490 (mm) cc_final: 0.7094 (tt) REVERT: B 198 HIS cc_start: 0.4769 (t70) cc_final: 0.4536 (t70) REVERT: B 325 LEU cc_start: 0.5933 (mt) cc_final: 0.5714 (mt) outliers start: 21 outliers final: 18 residues processed: 122 average time/residue: 0.1777 time to fit residues: 31.4944 Evaluate side-chains 123 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 174 GLN Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 chunk 95 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 81 optimal weight: 30.0000 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6177 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 8710 Z= 0.418 Angle : 0.860 12.744 11997 Z= 0.477 Chirality : 0.048 0.204 1302 Planarity : 0.007 0.119 1384 Dihedral : 17.089 102.149 1400 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.95 % Favored : 92.94 % Rotamer: Outliers : 2.99 % Allowed : 17.13 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.25 (0.27), residues: 921 helix: 0.39 (0.30), residues: 291 sheet: -1.86 (0.42), residues: 140 loop : -1.25 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP B 402 HIS 0.005 0.002 HIS A 315 PHE 0.028 0.004 PHE B 130 TYR 0.021 0.003 TYR B 339 ARG 0.006 0.001 ARG A 448 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 282 LEU cc_start: 0.6212 (OUTLIER) cc_final: 0.5805 (mt) REVERT: A 357 MET cc_start: 0.5655 (ttt) cc_final: 0.5320 (tpp) REVERT: B 24 TRP cc_start: 0.5781 (p90) cc_final: 0.4966 (p90) REVERT: B 174 GLN cc_start: 0.6442 (OUTLIER) cc_final: 0.5663 (mp10) REVERT: B 180 ILE cc_start: 0.7422 (mm) cc_final: 0.7027 (tt) REVERT: B 198 HIS cc_start: 0.5047 (t70) cc_final: 0.4813 (t70) outliers start: 25 outliers final: 18 residues processed: 125 average time/residue: 0.1731 time to fit residues: 31.5712 Evaluate side-chains 120 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 174 GLN Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 11 optimal weight: 0.1980 chunk 21 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 9 optimal weight: 0.0870 chunk 14 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 overall best weight: 2.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.219271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.177147 restraints weight = 9852.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.177722 restraints weight = 7666.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.179876 restraints weight = 6567.275| |-----------------------------------------------------------------------------| r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6171 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8710 Z= 0.194 Angle : 0.726 12.933 11997 Z= 0.412 Chirality : 0.042 0.147 1302 Planarity : 0.006 0.115 1384 Dihedral : 16.684 103.629 1400 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.34 % Favored : 95.55 % Rotamer: Outliers : 2.40 % Allowed : 17.84 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.62 (0.28), residues: 921 helix: 1.09 (0.31), residues: 287 sheet: -1.58 (0.41), residues: 150 loop : -0.91 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 402 HIS 0.004 0.001 HIS A 315 PHE 0.011 0.001 PHE B 130 TYR 0.023 0.002 TYR A 501 ARG 0.003 0.000 ARG B 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1605.57 seconds wall clock time: 30 minutes 20.21 seconds (1820.21 seconds total)