Starting phenix.real_space_refine on Thu Jan 18 09:59:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb0_21583/01_2024/6wb0_21583.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb0_21583/01_2024/6wb0_21583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb0_21583/01_2024/6wb0_21583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb0_21583/01_2024/6wb0_21583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb0_21583/01_2024/6wb0_21583.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb0_21583/01_2024/6wb0_21583.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 74 5.49 5 S 6 5.16 5 C 5186 2.51 5 N 1481 2.21 5 O 1771 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 448": "NH1" <-> "NH2" Residue "A TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 36": "OE1" <-> "OE2" Residue "B TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 194": "OE1" <-> "OE2" Residue "B TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 8518 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 3911 Classifications: {'peptide': 545} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 510} Chain breaks: 3 Unresolved non-hydrogen bonds: 546 Unresolved non-hydrogen angles: 667 Unresolved non-hydrogen dihedrals: 457 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 4, 'TYR:plan': 3, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 4, 'GLU:plan': 32, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 304 Chain: "B" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2979 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 30, 'TRANS': 372} Chain breaks: 2 Unresolved non-hydrogen bonds: 356 Unresolved non-hydrogen angles: 440 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 168 Chain: "C" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 747 Classifications: {'RNA': 35} Modifications used: {'5*END': 1, 'rna3p_pur': 20, 'rna3p_pyr': 14} Link IDs: {'rna3p': 34} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 881 Inner-chain residues flagged as termini: ['pdbres=" G D 46 "'] Classifications: {'DNA': 4, 'RNA': 38} Modifications used: {'5*END': 2, 'rna3p_pur': 15, 'rna3p_pyr': 21} Link IDs: {'rna3p': 41} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 5.56, per 1000 atoms: 0.65 Number of scatterers: 8518 At special positions: 0 Unit cell: (104.94, 107.06, 117.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 P 74 15.00 O 1771 8.00 N 1481 7.00 C 5186 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: 3.58 Conformation dependent library (CDL) restraints added in 1.6 seconds 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1786 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 11 sheets defined 39.6% alpha, 6.3% beta 39 base pairs and 40 stacking pairs defined. Time for finding SS restraints: 3.16 Creating SS restraints... Processing helix chain 'A' and resid 30 through 44 Processing helix chain 'A' and resid 77 through 84 removed outlier: 4.292A pdb=" N LYS A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 114 through 118 removed outlier: 3.779A pdb=" N VAL A 118 " --> pdb=" O TYR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 removed outlier: 4.256A pdb=" N LYS A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 175 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 194 through 211 removed outlier: 3.579A pdb=" N HIS A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 268 Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 363 through 383 Processing helix chain 'A' and resid 394 through 404 removed outlier: 3.514A pdb=" N TRP A 398 " --> pdb=" O GLN A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 489 removed outlier: 3.678A pdb=" N ASP A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 508 removed outlier: 4.217A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 527 removed outlier: 4.059A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 4.005A pdb=" N GLN A 547 " --> pdb=" O GLY A 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 44 removed outlier: 4.139A pdb=" N ALA B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 91 removed outlier: 6.165A pdb=" N ASP B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 103 Processing helix chain 'B' and resid 112 through 118 removed outlier: 3.504A pdb=" N VAL B 118 " --> pdb=" O TYR B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 4.140A pdb=" N LYS B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.815A pdb=" N ASN B 137 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 175 removed outlier: 5.158A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) Proline residue: B 170 - end of helix removed outlier: 3.883A pdb=" N GLN B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 212 removed outlier: 4.461A pdb=" N TRP B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 269 removed outlier: 3.944A pdb=" N GLN B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 285 removed outlier: 3.724A pdb=" N LYS B 281 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU B 282 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU B 283 " --> pdb=" O SER B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 312 removed outlier: 3.870A pdb=" N GLU B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 384 Processing helix chain 'B' and resid 394 through 402 removed outlier: 3.853A pdb=" N TRP B 398 " --> pdb=" O GLN B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 427 removed outlier: 3.519A pdb=" N TYR B 427 " --> pdb=" O LYS B 424 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 108 removed outlier: 3.866A pdb=" N GLY A 190 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL A 179 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 232 through 234 Processing sheet with id=AA3, first strand: chain 'A' and resid 326 through 329 removed outlier: 7.304A pdb=" N TYR A 339 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N THR A 351 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE A 341 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 389 through 391 Processing sheet with id=AA5, first strand: chain 'A' and resid 439 through 441 removed outlier: 6.524A pdb=" N PHE A 440 " --> pdb=" O VAL A 496 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 454 through 457 removed outlier: 3.569A pdb=" N LYS A 465 " --> pdb=" O TYR A 457 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 60 through 62 removed outlier: 4.539A pdb=" N PHE B 61 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU B 74 " --> pdb=" O PHE B 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 110 Processing sheet with id=AA9, first strand: chain 'B' and resid 129 through 131 removed outlier: 4.050A pdb=" N PHE B 130 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 252 through 253 removed outlier: 4.479A pdb=" N TRP B 252 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE B 293 " --> pdb=" O TRP B 252 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 337 through 339 removed outlier: 3.858A pdb=" N THR B 338 " --> pdb=" O GLN B 330 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN B 330 " --> pdb=" O THR B 338 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 390 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) 247 hydrogen bonds defined for protein. 687 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 101 hydrogen bonds 190 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 2.78 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2420 1.34 - 1.45: 1856 1.45 - 1.57: 4461 1.57 - 1.69: 147 1.69 - 1.81: 9 Bond restraints: 8893 Sorted by residual: bond pdb=" N PRO A 25 " pdb=" CD PRO A 25 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.65e+01 bond pdb=" C5 DC D 77 " pdb=" C6 DC D 77 " ideal model delta sigma weight residual 1.337 1.361 -0.024 2.00e-02 2.50e+03 1.41e+00 bond pdb=" C THR A 216 " pdb=" N PRO A 217 " ideal model delta sigma weight residual 1.326 1.341 -0.015 1.44e-02 4.82e+03 1.08e+00 bond pdb=" C GLU A 169 " pdb=" O GLU A 169 " ideal model delta sigma weight residual 1.241 1.231 0.010 9.80e-03 1.04e+04 1.07e+00 bond pdb=" CG PRO A 226 " pdb=" CD PRO A 226 " ideal model delta sigma weight residual 1.512 1.485 0.027 2.70e-02 1.37e+03 1.03e+00 ... (remaining 8888 not shown) Histogram of bond angle deviations from ideal: 100.90 - 107.54: 847 107.54 - 114.17: 5203 114.17 - 120.81: 3345 120.81 - 127.45: 2880 127.45 - 134.09: 274 Bond angle restraints: 12549 Sorted by residual: angle pdb=" CA PRO A 25 " pdb=" N PRO A 25 " pdb=" CD PRO A 25 " ideal model delta sigma weight residual 112.00 106.61 5.39 1.40e+00 5.10e-01 1.48e+01 angle pdb=" CA VAL A 467 " pdb=" C VAL A 467 " pdb=" N PRO A 468 " ideal model delta sigma weight residual 116.57 119.44 -2.87 9.80e-01 1.04e+00 8.61e+00 angle pdb=" N ILE B 180 " pdb=" CA ILE B 180 " pdb=" C ILE B 180 " ideal model delta sigma weight residual 108.48 112.47 -3.99 1.44e+00 4.82e-01 7.66e+00 angle pdb=" CA GLU A 169 " pdb=" C GLU A 169 " pdb=" N PRO A 170 " ideal model delta sigma weight residual 120.79 118.14 2.65 9.70e-01 1.06e+00 7.44e+00 angle pdb=" N LYS A 49 " pdb=" CA LYS A 49 " pdb=" C LYS A 49 " ideal model delta sigma weight residual 107.32 111.61 -4.29 1.65e+00 3.67e-01 6.75e+00 ... (remaining 12544 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 4803 17.60 - 35.21: 271 35.21 - 52.81: 113 52.81 - 70.42: 63 70.42 - 88.02: 27 Dihedral angle restraints: 5277 sinusoidal: 2516 harmonic: 2761 Sorted by residual: dihedral pdb=" O5' A D 50 " pdb=" C5' A D 50 " pdb=" C4' A D 50 " pdb=" C3' A D 50 " ideal model delta sinusoidal sigma weight residual -65.00 -7.52 -57.48 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CA LYS B 73 " pdb=" CB LYS B 73 " pdb=" CG LYS B 73 " pdb=" CD LYS B 73 " ideal model delta sinusoidal sigma weight residual 180.00 124.82 55.18 3 1.50e+01 4.44e-03 9.33e+00 dihedral pdb=" N PHE B 61 " pdb=" CA PHE B 61 " pdb=" CB PHE B 61 " pdb=" CG PHE B 61 " ideal model delta sinusoidal sigma weight residual 60.00 4.96 55.04 3 1.50e+01 4.44e-03 9.32e+00 ... (remaining 5274 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1176 0.037 - 0.074: 197 0.074 - 0.111: 84 0.111 - 0.148: 33 0.148 - 0.185: 4 Chirality restraints: 1494 Sorted by residual: chirality pdb=" C3' DT D 78 " pdb=" C4' DT D 78 " pdb=" O3' DT D 78 " pdb=" C2' DT D 78 " both_signs ideal model delta sigma weight residual False -2.66 -2.47 -0.19 2.00e-01 2.50e+01 8.58e-01 chirality pdb=" C3' DG D 73 " pdb=" C4' DG D 73 " pdb=" O3' DG D 73 " pdb=" C2' DG D 73 " both_signs ideal model delta sigma weight residual False -2.66 -2.48 -0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" C3' DC D 77 " pdb=" C4' DC D 77 " pdb=" O3' DC D 77 " pdb=" C2' DC D 77 " both_signs ideal model delta sigma weight residual False -2.66 -2.48 -0.18 2.00e-01 2.50e+01 8.25e-01 ... (remaining 1491 not shown) Planarity restraints: 1322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 58 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO B 59 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 59 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 59 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 168 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.84e+00 pdb=" C LEU A 168 " 0.023 2.00e-02 2.50e+03 pdb=" O LEU A 168 " -0.009 2.00e-02 2.50e+03 pdb=" N GLU A 169 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT D 78 " 0.010 2.00e-02 2.50e+03 7.49e-03 1.40e+00 pdb=" N1 DT D 78 " 0.009 2.00e-02 2.50e+03 pdb=" C2 DT D 78 " -0.002 2.00e-02 2.50e+03 pdb=" O2 DT D 78 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DT D 78 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DT D 78 " 0.001 2.00e-02 2.50e+03 pdb=" O4 DT D 78 " 0.012 2.00e-02 2.50e+03 pdb=" C5 DT D 78 " -0.006 2.00e-02 2.50e+03 pdb=" C7 DT D 78 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DT D 78 " -0.008 2.00e-02 2.50e+03 ... (remaining 1319 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 320 2.68 - 3.24: 8326 3.24 - 3.79: 13760 3.79 - 4.35: 17343 4.35 - 4.90: 26029 Nonbonded interactions: 65778 Sorted by model distance: nonbonded pdb=" C TYR A 339 " pdb=" OE1 GLN A 340 " model vdw 2.131 3.270 nonbonded pdb=" OP2 A C 203 " pdb=" N6 A D 50 " model vdw 2.218 2.520 nonbonded pdb=" NZ LYS A 350 " pdb=" OE2 GLU A 378 " model vdw 2.221 2.520 nonbonded pdb=" N PHE B 61 " pdb=" CD1 PHE B 61 " model vdw 2.232 3.420 nonbonded pdb=" O2' A D 50 " pdb=" OP2 G D 52 " model vdw 2.239 2.440 ... (remaining 65773 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: 1.870 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: 0.000 Extract box with map and model: 4.030 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 29.670 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 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 : 0.002 0.057 8893 Z= 0.133 Angle : 0.507 6.551 12549 Z= 0.289 Chirality : 0.039 0.185 1494 Planarity : 0.003 0.048 1322 Dihedral : 15.902 88.022 3491 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.81 % Allowed : 3.57 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -4.46 (0.24), residues: 934 helix: -1.57 (0.25), residues: 325 sheet: -4.91 (0.29), residues: 116 loop : -3.53 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.000 TRP A 402 HIS 0.001 0.000 HIS B 208 PHE 0.007 0.000 PHE A 227 TYR 0.004 0.000 TYR A 501 ARG 0.001 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 149 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 ILE cc_start: 0.8345 (mt) cc_final: 0.7329 (mt) REVERT: B 401 TRP cc_start: 0.8317 (m100) cc_final: 0.8098 (m100) outliers start: 5 outliers final: 4 residues processed: 154 average time/residue: 0.2715 time to fit residues: 53.3839 Evaluate side-chains 69 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 40 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 147 ASN A 394 GLN A 478 GLN A 519 ASN B 57 ASN B 198 HIS B 265 ASN B 373 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8893 Z= 0.297 Angle : 0.607 7.013 12549 Z= 0.309 Chirality : 0.042 0.178 1494 Planarity : 0.005 0.050 1322 Dihedral : 16.200 74.500 2113 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.76 (0.25), residues: 934 helix: -0.97 (0.27), residues: 336 sheet: -4.41 (0.26), residues: 159 loop : -2.95 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 426 HIS 0.003 0.001 HIS A 96 PHE 0.014 0.002 PHE A 227 TYR 0.016 0.002 TYR B 188 ARG 0.006 0.001 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8911 (pp30) cc_final: 0.8431 (pp30) REVERT: B 78 ARG cc_start: 0.8337 (mtm-85) cc_final: 0.7885 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1829 time to fit residues: 20.8459 Evaluate side-chains 47 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 62 optimal weight: 0.0070 chunk 25 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 99 optimal weight: 20.0000 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 GLN B 198 HIS B 265 ASN B 330 GLN B 373 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8893 Z= 0.156 Angle : 0.506 6.907 12549 Z= 0.252 Chirality : 0.039 0.148 1494 Planarity : 0.004 0.048 1322 Dihedral : 16.152 74.231 2113 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.00 (0.26), residues: 934 helix: -0.29 (0.28), residues: 339 sheet: -3.73 (0.30), residues: 159 loop : -2.69 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 402 HIS 0.003 0.001 HIS B 96 PHE 0.012 0.001 PHE A 227 TYR 0.010 0.001 TYR A 181 ARG 0.004 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8868 (pp30) cc_final: 0.8522 (pp30) REVERT: B 78 ARG cc_start: 0.8409 (mtm-85) cc_final: 0.8028 (ptp-110) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1720 time to fit residues: 20.8805 Evaluate side-chains 53 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 43 optimal weight: 0.0020 chunk 61 optimal weight: 0.5980 chunk 92 optimal weight: 0.0980 chunk 97 optimal weight: 20.0000 chunk 48 optimal weight: 0.1980 chunk 87 optimal weight: 0.0050 chunk 26 optimal weight: 0.3980 chunk 81 optimal weight: 0.0870 overall best weight: 0.0780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN B 198 HIS B 265 ASN B 373 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8893 Z= 0.119 Angle : 0.490 7.341 12549 Z= 0.235 Chirality : 0.038 0.156 1494 Planarity : 0.004 0.052 1322 Dihedral : 15.997 73.950 2113 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.43 (0.27), residues: 934 helix: 0.14 (0.30), residues: 339 sheet: -3.14 (0.33), residues: 158 loop : -2.44 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 402 HIS 0.003 0.001 HIS B 96 PHE 0.020 0.002 PHE B 124 TYR 0.017 0.001 TYR A 188 ARG 0.005 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8832 (pp30) cc_final: 0.8566 (pp30) REVERT: B 78 ARG cc_start: 0.8459 (mtm-85) cc_final: 0.8250 (ptp-110) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1640 time to fit residues: 21.6279 Evaluate side-chains 55 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 83 optimal weight: 0.0040 chunk 67 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 overall best weight: 4.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN B 373 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8893 Z= 0.360 Angle : 0.672 7.058 12549 Z= 0.343 Chirality : 0.042 0.151 1494 Planarity : 0.005 0.049 1322 Dihedral : 16.536 74.688 2113 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.75 (0.26), residues: 934 helix: -0.35 (0.28), residues: 330 sheet: -3.26 (0.32), residues: 170 loop : -2.35 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 426 HIS 0.004 0.001 HIS B 198 PHE 0.020 0.003 PHE A 160 TYR 0.032 0.003 TYR B 405 ARG 0.003 0.001 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8843 (pp30) cc_final: 0.8375 (pp30) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1781 time to fit residues: 15.8317 Evaluate side-chains 40 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 HIS ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN B 265 ASN B 348 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 8893 Z= 0.365 Angle : 0.643 7.024 12549 Z= 0.329 Chirality : 0.042 0.212 1494 Planarity : 0.005 0.040 1322 Dihedral : 16.756 74.564 2113 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.66 (0.26), residues: 934 helix: -0.36 (0.28), residues: 324 sheet: -3.11 (0.33), residues: 167 loop : -2.26 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 426 HIS 0.002 0.001 HIS A 96 PHE 0.021 0.003 PHE A 160 TYR 0.029 0.002 TYR B 405 ARG 0.010 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8860 (pp30) cc_final: 0.8389 (pp30) REVERT: B 369 THR cc_start: 0.9108 (p) cc_final: 0.8902 (t) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1757 time to fit residues: 13.9386 Evaluate side-chains 37 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.1980 chunk 55 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8893 Z= 0.144 Angle : 0.530 7.124 12549 Z= 0.260 Chirality : 0.039 0.154 1494 Planarity : 0.004 0.033 1322 Dihedral : 16.434 74.203 2113 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.03 (0.28), residues: 934 helix: 0.26 (0.30), residues: 326 sheet: -2.76 (0.35), residues: 163 loop : -2.00 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 402 HIS 0.003 0.001 HIS B 208 PHE 0.013 0.001 PHE A 227 TYR 0.017 0.001 TYR A 405 ARG 0.005 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8861 (pp30) cc_final: 0.8502 (pp30) REVERT: B 369 THR cc_start: 0.8976 (p) cc_final: 0.8727 (t) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1805 time to fit residues: 20.0456 Evaluate side-chains 44 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 85 optimal weight: 0.4980 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 361 HIS ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8893 Z= 0.261 Angle : 0.576 6.395 12549 Z= 0.290 Chirality : 0.040 0.148 1494 Planarity : 0.004 0.033 1322 Dihedral : 16.580 74.398 2113 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.15 (0.27), residues: 934 helix: 0.05 (0.29), residues: 326 sheet: -2.86 (0.35), residues: 169 loop : -1.92 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 153 HIS 0.003 0.001 HIS A 361 PHE 0.017 0.002 PHE A 160 TYR 0.022 0.002 TYR B 405 ARG 0.003 0.001 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8872 (pp30) cc_final: 0.8409 (pp30) REVERT: B 369 THR cc_start: 0.9051 (p) cc_final: 0.8805 (t) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1789 time to fit residues: 15.5464 Evaluate side-chains 37 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 27 optimal weight: 0.0170 chunk 81 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 59 optimal weight: 0.0170 chunk 95 optimal weight: 20.0000 chunk 58 optimal weight: 4.9990 overall best weight: 2.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8893 Z= 0.213 Angle : 0.547 6.937 12549 Z= 0.273 Chirality : 0.039 0.149 1494 Planarity : 0.004 0.033 1322 Dihedral : 16.527 74.324 2113 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.99 (0.28), residues: 934 helix: 0.14 (0.29), residues: 326 sheet: -2.72 (0.35), residues: 169 loop : -1.82 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 402 HIS 0.002 0.001 HIS B 208 PHE 0.014 0.002 PHE A 160 TYR 0.016 0.002 TYR B 405 ARG 0.002 0.000 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8901 (pp30) cc_final: 0.8549 (pp30) REVERT: B 369 THR cc_start: 0.9019 (p) cc_final: 0.8781 (t) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1624 time to fit residues: 14.1045 Evaluate side-chains 36 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 9.9990 chunk 66 optimal weight: 0.1980 chunk 100 optimal weight: 20.0000 chunk 92 optimal weight: 0.7980 chunk 80 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8893 Z= 0.302 Angle : 0.612 7.194 12549 Z= 0.310 Chirality : 0.040 0.149 1494 Planarity : 0.004 0.032 1322 Dihedral : 16.783 74.503 2113 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -2.19 (0.27), residues: 934 helix: -0.20 (0.28), residues: 334 sheet: -2.61 (0.37), residues: 167 loop : -1.92 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 426 HIS 0.002 0.001 HIS A 235 PHE 0.020 0.002 PHE A 87 TYR 0.026 0.002 TYR B 405 ARG 0.003 0.001 ARG B 125 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8925 (pp30) cc_final: 0.8446 (pp30) REVERT: A 364 ASP cc_start: 0.8045 (p0) cc_final: 0.7493 (p0) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1777 time to fit residues: 14.7251 Evaluate side-chains 37 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 33 optimal weight: 0.0670 chunk 82 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 70 optimal weight: 0.2980 chunk 4 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.4724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN B 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.077218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.064135 restraints weight = 50260.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.065231 restraints weight = 30142.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.065989 restraints weight = 21076.119| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8893 Z= 0.166 Angle : 0.535 7.222 12549 Z= 0.266 Chirality : 0.039 0.205 1494 Planarity : 0.004 0.035 1322 Dihedral : 16.518 74.226 2113 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -1.77 (0.28), residues: 934 helix: 0.20 (0.29), residues: 328 sheet: -2.28 (0.38), residues: 168 loop : -1.75 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 402 HIS 0.003 0.001 HIS B 208 PHE 0.013 0.002 PHE A 227 TYR 0.011 0.001 TYR B 405 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: 1598.78 seconds wall clock time: 29 minutes 58.64 seconds (1798.64 seconds total)