Starting phenix.real_space_refine on Tue Sep 24 20:57:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb0_21583/09_2024/6wb0_21583.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb0_21583/09_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_21583/09_2024/6wb0_21583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb0_21583/09_2024/6wb0_21583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb0_21583/09_2024/6wb0_21583.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb0_21583/09_2024/6wb0_21583.cif" } 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. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 6.04, per 1000 atoms: 0.71 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 - 3.00 Amino acid : True - 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: 2.57 Conformation dependent library (CDL) restraints added in 977.1 milliseconds 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: 3.35 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: 2.74 Time building geometry restraints manager: 2.91 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: 0.00 - 1.31: 12220 1.31 - 2.62: 240 2.62 - 3.93: 82 3.93 - 5.24: 4 5.24 - 6.55: 3 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 3.120 nonbonded pdb=" NZ LYS A 350 " pdb=" OE2 GLU A 378 " model vdw 2.221 3.120 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 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.870 Find NCS groups from input model: 0.090 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.560 ------------------------------------------------------------------------------- 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 : 0.790 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: 0.2691 time to fit residues: 52.8865 Evaluate side-chains 69 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 65 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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: 7.9990 chunk 42 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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 145 GLN B 198 HIS B 265 ASN B 330 GLN B 373 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 8893 Z= 0.434 Angle : 0.711 7.070 12549 Z= 0.365 Chirality : 0.044 0.171 1494 Planarity : 0.005 0.047 1322 Dihedral : 17.134 74.655 2169 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % 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: -4.15 (0.24), residues: 934 helix: -1.25 (0.26), residues: 334 sheet: -4.58 (0.24), residues: 171 loop : -3.15 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 24 HIS 0.004 0.001 HIS A 96 PHE 0.015 0.003 PHE A 227 TYR 0.021 0.003 TYR B 342 ARG 0.008 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 68 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8955 (pp30) cc_final: 0.8440 (pp30) REVERT: A 364 ASP cc_start: 0.8266 (p0) cc_final: 0.7184 (p0) REVERT: B 124 PHE cc_start: 0.8908 (t80) cc_final: 0.8680 (t80) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1762 time to fit residues: 17.6726 Evaluate side-chains 44 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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: 7.9990 chunk 28 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 99 optimal weight: 20.0000 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 73 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 HIS B 265 ASN B 373 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2989 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= 0.151 Angle : 0.522 6.801 12549 Z= 0.260 Chirality : 0.039 0.153 1494 Planarity : 0.004 0.050 1322 Dihedral : 16.956 74.294 2169 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % 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: -3.10 (0.26), residues: 934 helix: -0.40 (0.28), residues: 334 sheet: -3.84 (0.29), residues: 159 loop : -2.67 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 402 HIS 0.004 0.001 HIS A 361 PHE 0.013 0.001 PHE A 227 TYR 0.015 0.001 TYR A 188 ARG 0.006 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 : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8927 (pp30) cc_final: 0.8576 (pp30) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1729 time to fit residues: 20.7303 Evaluate side-chains 51 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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: 2.9990 chunk 10 optimal weight: 9.9990 chunk 43 optimal weight: 0.0010 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 97 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.5792 ------------------------------------------------------------------------------- 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: 0.7667 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8893 Z= 0.175 Angle : 0.520 7.477 12549 Z= 0.259 Chirality : 0.039 0.155 1494 Planarity : 0.004 0.052 1322 Dihedral : 16.908 74.279 2169 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % 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: -2.68 (0.27), residues: 934 helix: -0.19 (0.29), residues: 334 sheet: -3.42 (0.31), residues: 164 loop : -2.36 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 426 HIS 0.002 0.001 HIS B 96 PHE 0.013 0.001 PHE A 227 TYR 0.012 0.001 TYR B 405 ARG 0.008 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 77 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8883 (pp30) cc_final: 0.8448 (pp30) REVERT: A 409 THR cc_start: 0.9255 (p) cc_final: 0.9051 (p) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1609 time to fit residues: 18.8181 Evaluate side-chains 51 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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: 0.0040 chunk 1 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 67 optimal weight: 0.0670 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 overall best weight: 3.2136 ------------------------------------------------------------------------------- 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 B 373 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8893 Z= 0.294 Angle : 0.608 6.749 12549 Z= 0.308 Chirality : 0.041 0.198 1494 Planarity : 0.004 0.039 1322 Dihedral : 17.119 74.516 2169 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % 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: -2.68 (0.27), residues: 934 helix: -0.32 (0.29), residues: 332 sheet: -3.19 (0.33), residues: 158 loop : -2.37 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 426 HIS 0.007 0.001 HIS B 198 PHE 0.019 0.002 PHE A 160 TYR 0.025 0.002 TYR B 405 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 58 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.8304 (m-80) cc_final: 0.8070 (m-80) REVERT: A 182 GLN cc_start: 0.8886 (pp30) cc_final: 0.8426 (pp30) REVERT: B 376 THR cc_start: 0.9043 (p) cc_final: 0.8776 (p) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1698 time to fit residues: 14.9820 Evaluate side-chains 42 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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: 0.7980 chunk 19 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 94 optimal weight: 9.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- 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: 0.7759 moved from start: 0.4317 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 : 0.588 6.511 12549 Z= 0.297 Chirality : 0.041 0.208 1494 Planarity : 0.004 0.033 1322 Dihedral : 17.203 74.456 2169 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % 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: -2.54 (0.27), residues: 934 helix: -0.27 (0.29), residues: 335 sheet: -2.99 (0.34), residues: 157 loop : -2.29 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 153 HIS 0.002 0.001 HIS B 208 PHE 0.017 0.002 PHE A 160 TYR 0.022 0.002 TYR B 405 ARG 0.004 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 59 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.8332 (m-80) cc_final: 0.8104 (m-80) REVERT: A 182 GLN cc_start: 0.8973 (pp30) cc_final: 0.8523 (pp30) REVERT: A 230 MET cc_start: 0.8800 (mpp) cc_final: 0.8519 (mpp) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1668 time to fit residues: 15.0908 Evaluate side-chains 39 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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: 10.0000 chunk 55 optimal weight: 0.9990 chunk 71 optimal weight: 0.0270 chunk 82 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 overall best weight: 1.8044 ------------------------------------------------------------------------------- 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: 0.7733 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8893 Z= 0.187 Angle : 0.539 6.621 12549 Z= 0.267 Chirality : 0.039 0.150 1494 Planarity : 0.004 0.034 1322 Dihedral : 17.107 74.304 2169 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % 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: -2.11 (0.27), residues: 934 helix: 0.06 (0.29), residues: 327 sheet: -2.74 (0.35), residues: 157 loop : -1.97 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 402 HIS 0.002 0.001 HIS B 208 PHE 0.013 0.002 PHE B 124 TYR 0.014 0.001 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 56 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8982 (pp30) cc_final: 0.8527 (pp30) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1689 time to fit residues: 14.4453 Evaluate side-chains 40 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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: 1.9990 chunk 19 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 GLN B 265 ASN B 418 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.4479 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= 0.157 Angle : 0.521 6.579 12549 Z= 0.257 Chirality : 0.038 0.178 1494 Planarity : 0.004 0.038 1322 Dihedral : 17.008 74.207 2169 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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 (0.27), residues: 934 helix: 0.15 (0.29), residues: 336 sheet: -2.48 (0.37), residues: 157 loop : -1.96 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 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 B 115 ARG 0.006 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 63 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8947 (pp30) cc_final: 0.8491 (pp30) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1670 time to fit residues: 16.1258 Evaluate side-chains 40 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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: 0.9990 chunk 54 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 95 optimal weight: 20.0000 chunk 58 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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: 0.7715 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8893 Z= 0.156 Angle : 0.515 7.106 12549 Z= 0.252 Chirality : 0.038 0.152 1494 Planarity : 0.004 0.038 1322 Dihedral : 16.947 74.158 2169 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: -1.68 (0.28), residues: 934 helix: 0.34 (0.30), residues: 329 sheet: -2.24 (0.37), residues: 162 loop : -1.77 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 402 HIS 0.002 0.001 HIS B 208 PHE 0.013 0.001 PHE A 227 TYR 0.013 0.001 TYR B 115 ARG 0.006 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 : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8949 (pp30) cc_final: 0.8473 (pp30) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1816 time to fit residues: 16.8989 Evaluate side-chains 44 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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: 10.0000 chunk 66 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 92 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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: 0.7741 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8893 Z= 0.210 Angle : 0.545 6.966 12549 Z= 0.272 Chirality : 0.039 0.171 1494 Planarity : 0.004 0.037 1322 Dihedral : 16.996 74.236 2169 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % 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: -1.71 (0.28), residues: 934 helix: 0.30 (0.30), residues: 329 sheet: -2.22 (0.37), residues: 168 loop : -1.77 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 402 HIS 0.002 0.001 HIS B 208 PHE 0.015 0.002 PHE A 160 TYR 0.016 0.001 TYR B 405 ARG 0.003 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 60 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8957 (pp30) cc_final: 0.8482 (pp30) REVERT: A 364 ASP cc_start: 0.7896 (p0) cc_final: 0.7395 (p0) REVERT: A 367 GLN cc_start: 0.8559 (mp10) cc_final: 0.8271 (mp10) REVERT: B 78 ARG cc_start: 0.8701 (mpp80) cc_final: 0.8382 (mtp85) REVERT: B 369 THR cc_start: 0.9015 (p) cc_final: 0.8756 (t) REVERT: B 401 TRP cc_start: 0.8592 (m100) cc_final: 0.8200 (m100) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1661 time to fit residues: 15.5565 Evaluate side-chains 41 residues out of total 853 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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: 6.9990 chunk 11 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 14 optimal weight: 0.0770 chunk 70 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 HIS B 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.077158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.064086 restraints weight = 50422.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.065224 restraints weight = 29950.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.065975 restraints weight = 20618.299| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8893 Z= 0.244 Angle : 0.571 6.880 12549 Z= 0.288 Chirality : 0.039 0.167 1494 Planarity : 0.004 0.036 1322 Dihedral : 17.120 74.317 2169 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % 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: -1.79 (0.28), residues: 934 helix: 0.20 (0.29), residues: 330 sheet: -2.26 (0.38), residues: 168 loop : -1.80 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 153 HIS 0.004 0.001 HIS A 361 PHE 0.018 0.002 PHE A 160 TYR 0.020 0.002 TYR B 405 ARG 0.003 0.001 ARG B 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1505.37 seconds wall clock time: 27 minutes 50.74 seconds (1670.74 seconds total)