Starting phenix.real_space_refine on Fri Dec 8 12:54:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2h_14466/12_2023/7z2h_14466_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2h_14466/12_2023/7z2h_14466.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2h_14466/12_2023/7z2h_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_14466/12_2023/7z2h_14466_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2h_14466/12_2023/7z2h_14466_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2h_14466/12_2023/7z2h_14466.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2h_14466/12_2023/7z2h_14466.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2h_14466/12_2023/7z2h_14466_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z2h_14466/12_2023/7z2h_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-1.21rc1-5172/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: 4.89, 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: 3.32 Conformation dependent library (CDL) restraints added in 1.3 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: 3.74 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: 2.53 Time building geometry restraints manager: 3.62 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: 0.110 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: 0.930 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.580 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.020 ------------------------------------------------------------------------------- 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 : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 133 average time/residue: 0.2076 time to fit residues: 38.2752 Evaluate side-chains 105 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 0.892 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2270 time to fit residues: 1.9370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.1980 chunk 87 optimal weight: 0.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 GLN B 269 GLN B 418 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5984 moved from start: 0.0893 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= 0.194 Angle : 0.716 14.197 11997 Z= 0.411 Chirality : 0.042 0.182 1302 Planarity : 0.006 0.113 1384 Dihedral : 17.316 114.503 1398 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.58 % Favored : 96.20 % Rotamer: Outliers : 0.48 % Allowed : 7.66 % Favored : 91.86 % 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: -0.46 (0.28), residues: 921 helix: 1.11 (0.31), residues: 307 sheet: -1.42 (0.42), residues: 148 loop : -0.84 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 402 HIS 0.002 0.001 HIS A 315 PHE 0.010 0.001 PHE A 124 TYR 0.015 0.001 TYR A 501 ARG 0.003 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 0.874 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 116 average time/residue: 0.1822 time to fit residues: 30.6028 Evaluate side-chains 104 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 0.845 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0858 time to fit residues: 1.8792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 0.7980 chunk 27 optimal weight: 9.9990 chunk 72 optimal weight: 30.0000 chunk 59 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 86 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 overall best weight: 6.5588 ------------------------------------------------------------------------------- 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 A 361 HIS ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN B 255 ASN B 269 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6127 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8710 Z= 0.324 Angle : 0.789 13.194 11997 Z= 0.445 Chirality : 0.046 0.228 1302 Planarity : 0.007 0.118 1384 Dihedral : 17.280 106.650 1398 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.41 % Favored : 93.49 % Rotamer: Outliers : 2.40 % Allowed : 11.38 % Favored : 86.23 % 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: -0.86 (0.28), residues: 921 helix: 0.85 (0.30), residues: 291 sheet: -1.87 (0.42), residues: 136 loop : -1.03 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 229 HIS 0.006 0.002 HIS A 315 PHE 0.021 0.003 PHE B 130 TYR 0.018 0.002 TYR A 457 ARG 0.007 0.001 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: 20 poor density : 111 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 125 average time/residue: 0.1750 time to fit residues: 31.9067 Evaluate side-chains 117 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 0.886 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0829 time to fit residues: 3.2071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 58 optimal weight: 0.4980 chunk 87 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- 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: 0.6056 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8710 Z= 0.190 Angle : 0.699 13.150 11997 Z= 0.406 Chirality : 0.042 0.167 1302 Planarity : 0.006 0.114 1384 Dihedral : 16.945 107.627 1398 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.58 % Favored : 96.31 % Rotamer: Outliers : 0.72 % Allowed : 14.13 % Favored : 85.15 % 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: -0.51 (0.28), residues: 921 helix: 1.21 (0.31), residues: 288 sheet: -1.65 (0.41), residues: 148 loop : -0.82 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 402 HIS 0.002 0.001 HIS A 315 PHE 0.010 0.001 PHE B 130 TYR 0.015 0.001 TYR A 501 ARG 0.003 0.000 ARG B 72 *********************** 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 115 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 113 average time/residue: 0.1871 time to fit residues: 30.9355 Evaluate side-chains 103 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.939 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0826 time to fit residues: 1.4910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 30.0000 chunk 69 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 47 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 31 optimal weight: 0.0570 overall best weight: 4.3706 ------------------------------------------------------------------------------- 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: 0.6095 moved from start: 0.1900 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= 0.244 Angle : 0.734 12.950 11997 Z= 0.420 Chirality : 0.043 0.202 1302 Planarity : 0.006 0.116 1384 Dihedral : 16.931 105.383 1398 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.43 % Favored : 94.46 % Rotamer: Outliers : 1.32 % Allowed : 16.41 % Favored : 82.28 % 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: -0.66 (0.28), residues: 921 helix: 1.04 (0.31), residues: 289 sheet: -1.72 (0.41), residues: 149 loop : -0.89 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 402 HIS 0.004 0.001 HIS A 315 PHE 0.015 0.002 PHE B 130 TYR 0.014 0.002 TYR A 457 ARG 0.005 0.001 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 116 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 113 average time/residue: 0.1767 time to fit residues: 29.4234 Evaluate side-chains 108 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 0.927 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0837 time to fit residues: 2.3814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 54 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 7 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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: 0.6075 moved from start: 0.1976 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= 0.214 Angle : 0.707 12.874 11997 Z= 0.409 Chirality : 0.042 0.183 1302 Planarity : 0.006 0.115 1384 Dihedral : 16.813 104.924 1398 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.23 % Favored : 95.66 % Rotamer: Outliers : 0.96 % Allowed : 17.25 % Favored : 81.80 % 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: -0.58 (0.28), residues: 921 helix: 1.11 (0.31), residues: 288 sheet: -1.64 (0.41), residues: 148 loop : -0.85 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 402 HIS 0.003 0.001 HIS A 315 PHE 0.013 0.002 PHE B 130 TYR 0.012 0.002 TYR B 354 ARG 0.004 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 121 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 113 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 119 average time/residue: 0.1920 time to fit residues: 32.6269 Evaluate side-chains 112 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 107 time to evaluate : 0.824 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0846 time to fit residues: 1.9433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 92 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 42 optimal weight: 40.0000 chunk 36 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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: 0.6050 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8710 Z= 0.182 Angle : 0.698 12.920 11997 Z= 0.401 Chirality : 0.041 0.183 1302 Planarity : 0.006 0.114 1384 Dihedral : 16.652 104.250 1398 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.45 % Favored : 95.44 % Rotamer: Outliers : 1.44 % Allowed : 17.49 % Favored : 81.08 % 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: -0.43 (0.28), residues: 921 helix: 1.24 (0.31), residues: 288 sheet: -1.53 (0.42), residues: 148 loop : -0.77 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP B 402 HIS 0.002 0.001 HIS A 315 PHE 0.010 0.001 PHE B 130 TYR 0.010 0.001 TYR A 183 ARG 0.003 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 123 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 120 average time/residue: 0.1922 time to fit residues: 33.0232 Evaluate side-chains 109 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 0.880 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0820 time to fit residues: 2.0547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 58 optimal weight: 0.0570 chunk 63 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 72 optimal weight: 30.0000 chunk 84 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 overall best weight: 3.6106 ------------------------------------------------------------------------------- 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 174 GLN B 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6073 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8710 Z= 0.220 Angle : 0.723 12.846 11997 Z= 0.411 Chirality : 0.042 0.195 1302 Planarity : 0.006 0.116 1384 Dihedral : 16.687 103.597 1398 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.89 % Favored : 95.01 % Rotamer: Outliers : 0.48 % Allowed : 19.28 % 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: -0.52 (0.28), residues: 921 helix: 1.09 (0.31), residues: 290 sheet: -1.51 (0.42), residues: 148 loop : -0.80 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 402 HIS 0.003 0.001 HIS A 315 PHE 0.045 0.002 PHE A 160 TYR 0.012 0.001 TYR B 354 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 108 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 0.832 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 106 average time/residue: 0.2107 time to fit residues: 31.4603 Evaluate side-chains 105 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 0.927 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3288 time to fit residues: 2.0855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 51 optimal weight: 0.2980 chunk 37 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 77 optimal weight: 0.0670 chunk 81 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 chunk 56 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 overall best weight: 3.6724 ------------------------------------------------------------------------------- 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 174 GLN B 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6078 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8710 Z= 0.220 Angle : 0.725 12.824 11997 Z= 0.412 Chirality : 0.042 0.195 1302 Planarity : 0.006 0.116 1384 Dihedral : 16.674 103.033 1398 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.21 % Favored : 94.68 % Rotamer: Outliers : 0.48 % Allowed : 19.52 % Favored : 80.00 % 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: -0.55 (0.28), residues: 921 helix: 1.03 (0.31), residues: 291 sheet: -1.47 (0.43), residues: 148 loop : -0.83 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 402 HIS 0.004 0.001 HIS A 315 PHE 0.033 0.002 PHE A 160 TYR 0.012 0.002 TYR B 354 ARG 0.003 0.000 ARG A 448 *********************** 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 108 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 1.022 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 107 average time/residue: 0.1972 time to fit residues: 29.9719 Evaluate side-chains 106 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 103 time to evaluate : 0.859 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0872 time to fit residues: 1.6246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 6.9990 chunk 43 optimal weight: 0.0970 chunk 63 optimal weight: 0.0980 chunk 95 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 58 optimal weight: 0.4980 chunk 46 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 81 optimal weight: 20.0000 overall best weight: 1.6980 ------------------------------------------------------------------------------- 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 174 GLN B 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6031 moved from start: 0.2338 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= 0.174 Angle : 0.698 12.927 11997 Z= 0.400 Chirality : 0.041 0.164 1302 Planarity : 0.006 0.115 1384 Dihedral : 16.508 102.966 1398 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.67 % Favored : 95.22 % Rotamer: Outliers : 0.36 % Allowed : 19.64 % Favored : 80.00 % 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: -0.40 (0.29), residues: 921 helix: 1.07 (0.31), residues: 297 sheet: -1.31 (0.44), residues: 148 loop : -0.72 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 402 HIS 0.002 0.001 HIS A 315 PHE 0.019 0.001 PHE A 160 TYR 0.012 0.001 TYR A 501 ARG 0.012 0.001 ARG B 83 ********************** 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 115 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 112 time to evaluate : 0.990 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 115 average time/residue: 0.1930 time to fit residues: 31.6119 Evaluate side-chains 110 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 0.941 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0796 time to fit residues: 1.4608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 11 optimal weight: 30.0000 chunk 21 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 258 GLN A 348 ASN ** B 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.215895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.178533 restraints weight = 9961.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.176220 restraints weight = 12579.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.178262 restraints weight = 10551.914| |-----------------------------------------------------------------------------| r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8710 Z= 0.347 Angle : 0.814 12.747 11997 Z= 0.454 Chirality : 0.047 0.235 1302 Planarity : 0.007 0.118 1384 Dihedral : 16.861 100.746 1398 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.62 % Favored : 93.27 % Rotamer: Outliers : 0.24 % Allowed : 20.00 % 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: -0.95 (0.28), residues: 921 helix: 0.64 (0.30), residues: 289 sheet: -1.62 (0.43), residues: 149 loop : -1.05 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 402 HIS 0.004 0.001 HIS A 315 PHE 0.024 0.003 PHE A 160 TYR 0.018 0.002 TYR B 339 ARG 0.006 0.001 ARG A 448 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1577.12 seconds wall clock time: 30 minutes 1.81 seconds (1801.81 seconds total)