Starting phenix.real_space_refine on Mon Mar 11 14:35:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb0_21583/03_2024/6wb0_21583.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb0_21583/03_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_21583/03_2024/6wb0_21583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb0_21583/03_2024/6wb0_21583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb0_21583/03_2024/6wb0_21583.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb0_21583/03_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.26, per 1000 atoms: 0.62 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: 3.63 Conformation dependent library (CDL) restraints added in 1.5 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: 3.00 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: 2.70 Time building geometry restraints manager: 3.93 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: 4820 17.60 - 35.21: 292 35.21 - 52.81: 116 52.81 - 70.42: 78 70.42 - 88.02: 27 Dihedral angle restraints: 5333 sinusoidal: 2572 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 5330 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: 0.920 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: 4.120 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 28.350 Find NCS groups from input model: 0.200 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.400 ------------------------------------------------------------------------------- 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 : 16.404 88.022 3547 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 : 0.940 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: 0.2650 time to fit residues: 52.1377 Evaluate side-chains 69 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 HIS B 265 ASN B 373 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8893 Z= 0.304 Angle : 0.632 6.991 12549 Z= 0.324 Chirality : 0.042 0.183 1494 Planarity : 0.005 0.053 1322 Dihedral : 16.940 74.503 2169 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % 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: -3.82 (0.25), residues: 934 helix: -1.00 (0.27), residues: 338 sheet: -4.41 (0.26), residues: 165 loop : -2.98 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 426 HIS 0.004 0.001 HIS A 96 PHE 0.015 0.003 PHE A 227 TYR 0.018 0.002 TYR B 188 ARG 0.007 0.001 ARG B 83 *********************** 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 75 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8912 (pp30) cc_final: 0.8426 (pp30) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1880 time to fit residues: 20.8223 Evaluate side-chains 46 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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: 4.9990 chunk 28 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 99 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN B 57 ASN B 145 GLN B 265 ASN B 330 GLN B 373 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8893 Z= 0.265 Angle : 0.564 6.854 12549 Z= 0.288 Chirality : 0.040 0.145 1494 Planarity : 0.004 0.048 1322 Dihedral : 17.090 74.396 2169 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % 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: -3.17 (0.26), residues: 934 helix: -0.53 (0.28), residues: 340 sheet: -3.74 (0.30), residues: 159 loop : -2.74 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 426 HIS 0.006 0.002 HIS A 361 PHE 0.013 0.002 PHE A 227 TYR 0.020 0.002 TYR B 405 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 67 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8893 (pp30) cc_final: 0.8450 (pp30) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1710 time to fit residues: 17.2806 Evaluate side-chains 48 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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: 7.9990 chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 87 optimal weight: 0.0030 chunk 26 optimal weight: 4.9990 chunk 81 optimal weight: 20.0000 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 520 GLN B 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8893 Z= 0.229 Angle : 0.548 7.310 12549 Z= 0.274 Chirality : 0.039 0.153 1494 Planarity : 0.004 0.039 1322 Dihedral : 17.122 74.330 2169 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % 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: -2.79 (0.27), residues: 934 helix: -0.25 (0.29), residues: 334 sheet: -3.45 (0.31), residues: 164 loop : -2.47 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 426 HIS 0.003 0.001 HIS B 96 PHE 0.013 0.002 PHE A 227 TYR 0.017 0.002 TYR B 405 ARG 0.009 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 66 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8921 (pp30) cc_final: 0.8461 (pp30) REVERT: B 369 THR cc_start: 0.9055 (p) cc_final: 0.8816 (t) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1782 time to fit residues: 17.5992 Evaluate side-chains 42 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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: 0.9990 chunk 1 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 0.0870 chunk 83 optimal weight: 8.9990 chunk 67 optimal weight: 0.0070 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8893 Z= 0.147 Angle : 0.508 6.394 12549 Z= 0.250 Chirality : 0.039 0.178 1494 Planarity : 0.004 0.036 1322 Dihedral : 17.079 74.159 2169 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % 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: -2.28 (0.27), residues: 934 helix: 0.09 (0.29), residues: 333 sheet: -3.02 (0.34), residues: 164 loop : -2.15 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 402 HIS 0.003 0.001 HIS B 96 PHE 0.013 0.001 PHE A 227 TYR 0.015 0.001 TYR A 181 ARG 0.004 0.001 ARG B 78 *********************** 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 72 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8908 (pp30) cc_final: 0.8464 (pp30) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1708 time to fit residues: 18.6841 Evaluate side-chains 45 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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: 9.9990 chunk 19 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 51 optimal weight: 0.0010 chunk 94 optimal weight: 9.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 ASN B 348 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8893 Z= 0.278 Angle : 0.583 6.526 12549 Z= 0.293 Chirality : 0.040 0.158 1494 Planarity : 0.004 0.040 1322 Dihedral : 17.310 74.467 2169 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % 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: -2.29 (0.27), residues: 934 helix: 0.04 (0.30), residues: 325 sheet: -2.88 (0.35), residues: 163 loop : -2.15 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 426 HIS 0.003 0.001 HIS B 96 PHE 0.015 0.002 PHE A 87 TYR 0.015 0.002 TYR B 342 ARG 0.005 0.001 ARG B 199 *********************** 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 56 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8909 (pp30) cc_final: 0.8449 (pp30) REVERT: A 230 MET cc_start: 0.8906 (mpp) cc_final: 0.8502 (mpp) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1846 time to fit residues: 16.0592 Evaluate side-chains 39 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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: 9.9990 chunk 55 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 60 optimal weight: 0.1980 chunk 59 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 ASN B 418 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8893 Z= 0.252 Angle : 0.565 6.319 12549 Z= 0.286 Chirality : 0.040 0.147 1494 Planarity : 0.004 0.042 1322 Dihedral : 17.330 74.400 2169 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % 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: -2.13 (0.27), residues: 934 helix: 0.09 (0.29), residues: 327 sheet: -2.68 (0.36), residues: 163 loop : -2.04 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 410 HIS 0.002 0.001 HIS B 96 PHE 0.012 0.002 PHE A 227 TYR 0.023 0.002 TYR B 405 ARG 0.004 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 58 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8954 (pp30) cc_final: 0.8492 (pp30) REVERT: B 369 THR cc_start: 0.9023 (p) cc_final: 0.8784 (t) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1856 time to fit residues: 16.1436 Evaluate side-chains 38 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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: 0.6980 chunk 19 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 88 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4641 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= 0.207 Angle : 0.551 6.595 12549 Z= 0.275 Chirality : 0.039 0.151 1494 Planarity : 0.004 0.039 1322 Dihedral : 17.273 74.332 2169 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % 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: -1.95 (0.28), residues: 934 helix: 0.17 (0.30), residues: 328 sheet: -2.47 (0.38), residues: 163 loop : -1.93 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 426 HIS 0.002 0.001 HIS B 96 PHE 0.015 0.002 PHE A 227 TYR 0.016 0.001 TYR B 405 ARG 0.007 0.001 ARG B 78 *********************** 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 : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8943 (pp30) cc_final: 0.8470 (pp30) REVERT: A 367 GLN cc_start: 0.8232 (mp10) cc_final: 0.7934 (mp10) REVERT: B 369 THR cc_start: 0.9008 (p) cc_final: 0.8770 (t) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1779 time to fit residues: 15.1970 Evaluate side-chains 41 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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: 4.9990 chunk 93 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 59 optimal weight: 0.0980 chunk 95 optimal weight: 20.0000 chunk 58 optimal weight: 7.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8893 Z= 0.187 Angle : 0.530 6.915 12549 Z= 0.262 Chirality : 0.038 0.152 1494 Planarity : 0.004 0.031 1322 Dihedral : 17.180 74.263 2169 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % 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: -1.74 (0.28), residues: 934 helix: 0.25 (0.30), residues: 328 sheet: -2.16 (0.39), residues: 162 loop : -1.83 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 402 HIS 0.002 0.001 HIS B 208 PHE 0.013 0.001 PHE A 227 TYR 0.014 0.001 TYR B 405 ARG 0.007 0.001 ARG B 78 *********************** 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 63 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8930 (pp30) cc_final: 0.8462 (pp30) REVERT: A 364 ASP cc_start: 0.7927 (p0) cc_final: 0.7331 (p0) REVERT: A 367 GLN cc_start: 0.8417 (mp10) cc_final: 0.8150 (mp10) REVERT: A 493 VAL cc_start: 0.8473 (p) cc_final: 0.8200 (t) REVERT: B 369 THR cc_start: 0.9037 (p) cc_final: 0.8801 (t) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1692 time to fit residues: 16.3602 Evaluate side-chains 46 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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: 4.9990 chunk 66 optimal weight: 3.9990 chunk 100 optimal weight: 20.0000 chunk 92 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8893 Z= 0.281 Angle : 0.589 6.803 12549 Z= 0.296 Chirality : 0.040 0.149 1494 Planarity : 0.004 0.033 1322 Dihedral : 17.348 74.419 2169 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % 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: -1.96 (0.28), residues: 934 helix: 0.01 (0.29), residues: 328 sheet: -2.35 (0.38), residues: 163 loop : -1.86 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 426 HIS 0.002 0.001 HIS A 96 PHE 0.014 0.002 PHE A 160 TYR 0.016 0.002 TYR A 127 ARG 0.005 0.001 ARG B 78 ********************** 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 55 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8925 (pp30) cc_final: 0.8467 (pp30) REVERT: A 364 ASP cc_start: 0.7996 (p0) cc_final: 0.7377 (p0) REVERT: A 367 GLN cc_start: 0.8389 (mp10) cc_final: 0.8067 (mp10) REVERT: B 369 THR cc_start: 0.9121 (p) cc_final: 0.8885 (t) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1769 time to fit residues: 14.9989 Evaluate side-chains 41 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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: 1.9990 chunk 11 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.077230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.064141 restraints weight = 50338.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.065272 restraints weight = 30208.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.066018 restraints weight = 20931.284| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.5087 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= 0.204 Angle : 0.547 7.021 12549 Z= 0.272 Chirality : 0.039 0.151 1494 Planarity : 0.004 0.032 1322 Dihedral : 17.255 74.293 2169 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.79 (0.28), residues: 934 helix: 0.15 (0.29), residues: 329 sheet: -2.29 (0.38), residues: 163 loop : -1.74 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 402 HIS 0.002 0.001 HIS B 208 PHE 0.013 0.001 PHE A 227 TYR 0.012 0.001 TYR A 127 ARG 0.004 0.001 ARG B 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1576.91 seconds wall clock time: 29 minutes 42.02 seconds (1782.02 seconds total)