Starting phenix.real_space_refine on Thu Feb 13 01:40:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wb1_21584/02_2025/6wb1_21584.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wb1_21584/02_2025/6wb1_21584.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wb1_21584/02_2025/6wb1_21584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wb1_21584/02_2025/6wb1_21584.map" model { file = "/net/cci-nas-00/data/ceres_data/6wb1_21584/02_2025/6wb1_21584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wb1_21584/02_2025/6wb1_21584.cif" } resolution = 4.7 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= 0.003 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 72 5.49 5 S 5 5.16 5 C 5029 2.51 5 N 1444 2.21 5 O 1685 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8235 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 705 Classifications: {'RNA': 33} Modifications used: {'5*END': 1, 'rna3p_pur': 19, 'rna3p_pyr': 13} Link IDs: {'rna3p': 32} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 880 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: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 3716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 3716 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 196} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 507} Chain breaks: 3 Unresolved non-hydrogen bonds: 716 Unresolved non-hydrogen angles: 883 Unresolved non-hydrogen dihedrals: 575 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 16, 'PHE:plan': 5, 'GLU:plan': 40, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 397 Chain: "B" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 2934 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 30, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 396 Unresolved non-hydrogen angles: 488 Unresolved non-hydrogen dihedrals: 323 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 27, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 228 Time building chain proxies: 5.46, per 1000 atoms: 0.66 Number of scatterers: 8235 At special positions: 0 Unit cell: (99.64, 97.52, 119.78, 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 5 16.00 P 72 15.00 O 1685 8.00 N 1444 7.00 C 5029 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: 2.39 Conformation dependent library (CDL) restraints added in 848.9 milliseconds 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1782 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 39.2% alpha, 7.0% beta 38 base pairs and 40 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... Processing helix chain 'A' and resid 29 through 44 removed outlier: 3.706A pdb=" N ALA A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.611A pdb=" N VAL A 118 " --> pdb=" O TYR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 removed outlier: 3.745A 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: 3.558A pdb=" N HIS A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 269 Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 296 through 311 Processing helix chain 'A' and resid 363 through 383 removed outlier: 3.624A pdb=" N GLN A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 405 removed outlier: 3.693A pdb=" N TRP A 398 " --> pdb=" O GLN A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 489 removed outlier: 3.600A pdb=" N ASP A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.542A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 removed outlier: 3.591A pdb=" N ASN A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 553 Processing helix chain 'B' and resid 27 through 44 removed outlier: 4.051A pdb=" N ALA B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 91 removed outlier: 6.232A pdb=" N ASP B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N PHE B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TRP B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 103 removed outlier: 3.751A pdb=" N LYS B 101 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 124 through 129 removed outlier: 3.810A pdb=" N ALA B 129 " --> pdb=" O LYS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 154 through 175 removed outlier: 3.553A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Proline residue: B 170 - end of helix removed outlier: 3.772A pdb=" N LYS B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 211 Processing helix chain 'B' and resid 253 through 268 Processing helix chain 'B' and resid 276 through 284 removed outlier: 3.509A pdb=" N LYS B 281 " --> pdb=" O ARG B 277 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 312 removed outlier: 3.725A pdb=" N GLU B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 384 removed outlier: 3.738A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 removed outlier: 3.839A pdb=" N TRP B 398 " --> pdb=" O GLN B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 427 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 63 Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 107 removed outlier: 3.893A pdb=" N GLY A 190 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL A 179 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 232 through 233 Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 351 removed outlier: 6.884A pdb=" N ILE A 341 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA A 327 " --> pdb=" O LYS A 390 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.714A pdb=" N LYS A 512 " --> pdb=" O THR A 362 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 439 through 441 removed outlier: 6.283A pdb=" N PHE A 440 " --> pdb=" O VAL A 496 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 443 through 444 removed outlier: 4.028A pdb=" N ASP A 443 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY A 456 " --> pdb=" O ASP A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 49 removed outlier: 3.792A pdb=" N ILE B 142 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE B 132 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE B 130 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 106 through 107 Processing sheet with id=AB2, first strand: chain 'B' and resid 180 through 181 removed outlier: 3.847A pdb=" N TYR B 181 " --> pdb=" O TYR B 188 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 348 through 350 removed outlier: 7.107A pdb=" N ILE B 341 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLN B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR B 338 " --> pdb=" O GLN B 330 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN B 330 " --> pdb=" O THR B 338 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) 260 hydrogen bonds defined for protein. 711 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 99 hydrogen bonds 186 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 2.76 Time building geometry restraints manager: 2.70 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: 2221 1.34 - 1.45: 1911 1.45 - 1.57: 4322 1.57 - 1.69: 143 1.69 - 1.81: 8 Bond restraints: 8605 Sorted by residual: bond pdb=" C5 DC D 77 " pdb=" C6 DC D 77 " ideal model delta sigma weight residual 1.337 1.360 -0.023 2.00e-02 2.50e+03 1.37e+00 bond pdb=" CG PRO A 226 " pdb=" CD PRO A 226 " ideal model delta sigma weight residual 1.512 1.483 0.029 2.70e-02 1.37e+03 1.14e+00 bond pdb=" CA GLN B 332 " pdb=" C GLN B 332 " ideal model delta sigma weight residual 1.519 1.530 -0.011 1.01e-02 9.80e+03 1.09e+00 bond pdb=" C LEU B 149 " pdb=" N PRO B 150 " ideal model delta sigma weight residual 1.326 1.341 -0.015 1.44e-02 4.82e+03 1.08e+00 bond pdb=" C LEU A 149 " pdb=" N PRO A 150 " ideal model delta sigma weight residual 1.326 1.340 -0.014 1.44e-02 4.82e+03 9.61e-01 ... (remaining 8600 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 11952 1.47 - 2.95: 155 2.95 - 4.42: 60 4.42 - 5.89: 2 5.89 - 7.36: 1 Bond angle restraints: 12170 Sorted by residual: angle pdb=" N VAL A 276 " pdb=" CA VAL A 276 " pdb=" C VAL A 276 " ideal model delta sigma weight residual 113.20 109.76 3.44 9.60e-01 1.09e+00 1.29e+01 angle pdb=" CA LYS B 13 " pdb=" C LYS B 13 " pdb=" N PRO B 14 " ideal model delta sigma weight residual 118.83 116.42 2.41 8.70e-01 1.32e+00 7.69e+00 angle pdb=" N TYR A 115 " pdb=" CA TYR A 115 " pdb=" C TYR A 115 " ideal model delta sigma weight residual 111.07 108.19 2.88 1.07e+00 8.73e-01 7.24e+00 angle pdb=" C2' C C 134 " pdb=" C1' C C 134 " pdb=" N1 C C 134 " ideal model delta sigma weight residual 112.40 119.76 -7.36 3.00e+00 1.11e-01 6.02e+00 angle pdb=" N ARG A 307 " pdb=" CA ARG A 307 " pdb=" C ARG A 307 " ideal model delta sigma weight residual 111.07 108.64 2.43 1.07e+00 8.73e-01 5.17e+00 ... (remaining 12165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 4602 17.79 - 35.58: 289 35.58 - 53.37: 120 53.37 - 71.16: 87 71.16 - 88.95: 27 Dihedral angle restraints: 5125 sinusoidal: 2372 harmonic: 2753 Sorted by residual: dihedral pdb=" N GLU B 378 " pdb=" CA GLU B 378 " pdb=" CB GLU B 378 " pdb=" CG GLU B 378 " ideal model delta sinusoidal sigma weight residual -60.00 -114.88 54.88 3 1.50e+01 4.44e-03 9.31e+00 dihedral pdb=" O5' U C 135 " pdb=" C5' U C 135 " pdb=" C4' U C 135 " pdb=" C3' U C 135 " ideal model delta sinusoidal sigma weight residual 175.00 122.72 52.28 3 1.50e+01 4.44e-03 9.10e+00 dihedral pdb=" N GLU B 79 " pdb=" CA GLU B 79 " pdb=" CB GLU B 79 " pdb=" CG GLU B 79 " ideal model delta sinusoidal sigma weight residual -60.00 -110.51 50.51 3 1.50e+01 4.44e-03 8.91e+00 ... (remaining 5122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1226 0.045 - 0.091: 158 0.091 - 0.136: 74 0.136 - 0.181: 2 0.181 - 0.227: 3 Chirality restraints: 1463 Sorted by residual: chirality pdb=" C1' C C 134 " pdb=" O4' C C 134 " pdb=" C2' C C 134 " pdb=" N1 C C 134 " both_signs ideal model delta sigma weight residual False 2.46 2.23 0.23 2.00e-01 2.50e+01 1.28e+00 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 8.80e-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 8.32e-01 ... (remaining 1460 not shown) Planarity restraints: 1272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 224 " 0.037 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO A 225 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 225 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 225 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 257 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C ILE A 257 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE A 257 " -0.012 2.00e-02 2.50e+03 pdb=" N CYS A 258 " -0.011 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 7.34e-03 1.35e+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 " -0.009 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 " -0.005 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 1269 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 984 2.74 - 3.28: 8367 3.28 - 3.82: 14066 3.82 - 4.36: 15575 4.36 - 4.90: 24636 Nonbonded interactions: 63628 Sorted by model distance: nonbonded pdb=" O PRO B 321 " pdb=" NZ LYS B 385 " model vdw 2.204 3.120 nonbonded pdb=" O ARG A 211 " pdb=" NE ARG A 211 " model vdw 2.224 3.120 nonbonded pdb=" OG SER A 105 " pdb=" OG SER A 191 " model vdw 2.231 3.040 nonbonded pdb=" O ALA A 538 " pdb=" NZ LYS A 540 " model vdw 2.273 3.120 nonbonded pdb=" O TRP A 239 " pdb=" N GLY A 316 " model vdw 2.302 3.120 ... (remaining 63623 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: 0.970 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.230 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 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 0.029 8605 Z= 0.130 Angle : 0.500 7.364 12170 Z= 0.273 Chirality : 0.039 0.227 1463 Planarity : 0.003 0.055 1272 Dihedral : 17.215 88.947 3343 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.54 % Favored : 95.36 % Rotamer: Outliers : 0.55 % Allowed : 1.28 % Favored : 98.18 % 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: -4.82 (0.23), residues: 926 helix: -1.78 (0.24), residues: 325 sheet: -4.65 (0.28), residues: 147 loop : -3.82 (0.24), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 402 HIS 0.003 0.000 HIS A 208 PHE 0.006 0.001 PHE A 227 TYR 0.010 0.001 TYR B 354 ARG 0.002 0.000 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 103 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 PHE cc_start: 0.9239 (t80) cc_final: 0.8991 (t80) REVERT: A 366 LYS cc_start: 0.9720 (tppp) cc_final: 0.9463 (mptt) REVERT: B 42 GLU cc_start: 0.9454 (tt0) cc_final: 0.9181 (tt0) REVERT: B 206 ARG cc_start: 0.9155 (mtp180) cc_final: 0.8939 (ttm170) REVERT: B 307 ARG cc_start: 0.9207 (mtm180) cc_final: 0.8986 (mtt-85) REVERT: B 320 ASP cc_start: 0.8915 (t0) cc_final: 0.8593 (t70) REVERT: B 378 GLU cc_start: 0.9395 (OUTLIER) cc_final: 0.9193 (mt-10) outliers start: 3 outliers final: 0 residues processed: 104 average time/residue: 0.2761 time to fit residues: 36.6812 Evaluate side-chains 55 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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: 3.9990 chunk 76 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 51 optimal weight: 0.0970 chunk 40 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN A 475 GLN B 57 ASN B 161 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.061071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.049807 restraints weight = 63227.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.050906 restraints weight = 40076.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.051720 restraints weight = 28104.574| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8605 Z= 0.153 Angle : 0.528 7.904 12170 Z= 0.258 Chirality : 0.038 0.150 1463 Planarity : 0.004 0.064 1272 Dihedral : 18.360 86.602 2135 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.18 % Allowed : 1.64 % Favored : 98.18 % 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: -3.37 (0.26), residues: 926 helix: -0.41 (0.28), residues: 342 sheet: -3.66 (0.35), residues: 130 loop : -3.35 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 402 HIS 0.002 0.001 HIS B 235 PHE 0.011 0.002 PHE B 130 TYR 0.014 0.001 TYR B 146 ARG 0.008 0.001 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ARG cc_start: 0.9057 (ttm110) cc_final: 0.8505 (tpt90) REVERT: B 41 MET cc_start: 0.8504 (mtm) cc_final: 0.8266 (mtt) REVERT: B 42 GLU cc_start: 0.9469 (tt0) cc_final: 0.9232 (tt0) REVERT: B 206 ARG cc_start: 0.9260 (mtp180) cc_final: 0.9051 (ttm170) REVERT: B 320 ASP cc_start: 0.8959 (t0) cc_final: 0.8710 (t70) outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 0.2161 time to fit residues: 21.0367 Evaluate side-chains 52 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 83 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 73 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 35 optimal weight: 0.0060 chunk 47 optimal weight: 0.9990 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN A 545 ASN B 147 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.057806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.046131 restraints weight = 63000.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.047251 restraints weight = 39279.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.048043 restraints weight = 27184.541| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8605 Z= 0.187 Angle : 0.521 8.010 12170 Z= 0.255 Chirality : 0.037 0.130 1463 Planarity : 0.004 0.059 1272 Dihedral : 18.426 89.100 2135 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.18 % Allowed : 2.19 % Favored : 97.63 % 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: -2.40 (0.27), residues: 926 helix: 0.39 (0.29), residues: 343 sheet: -3.00 (0.37), residues: 130 loop : -2.82 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 410 HIS 0.003 0.001 HIS B 235 PHE 0.025 0.002 PHE B 416 TYR 0.013 0.001 TYR A 501 ARG 0.007 0.001 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ARG cc_start: 0.9057 (ttm110) cc_final: 0.8556 (tpt90) REVERT: B 42 GLU cc_start: 0.9447 (tt0) cc_final: 0.9208 (tt0) REVERT: B 320 ASP cc_start: 0.8875 (t0) cc_final: 0.8610 (t70) outliers start: 1 outliers final: 0 residues processed: 62 average time/residue: 0.2109 time to fit residues: 18.2831 Evaluate side-chains 48 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 44 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 145 GLN B 330 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.053188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.042245 restraints weight = 66478.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.043198 restraints weight = 41809.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.043865 restraints weight = 29349.197| |-----------------------------------------------------------------------------| r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8605 Z= 0.280 Angle : 0.607 13.022 12170 Z= 0.299 Chirality : 0.039 0.211 1463 Planarity : 0.005 0.062 1272 Dihedral : 18.821 92.928 2135 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % 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: -2.07 (0.27), residues: 926 helix: 0.37 (0.29), residues: 349 sheet: -2.51 (0.40), residues: 128 loop : -2.51 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 410 HIS 0.005 0.001 HIS B 235 PHE 0.015 0.002 PHE B 346 TYR 0.022 0.002 TYR B 146 ARG 0.006 0.001 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 MET cc_start: 0.8743 (mtm) cc_final: 0.8467 (mtt) REVERT: B 42 GLU cc_start: 0.9379 (tt0) cc_final: 0.9157 (tt0) REVERT: B 183 TYR cc_start: 0.8780 (t80) cc_final: 0.8392 (t80) REVERT: B 320 ASP cc_start: 0.8730 (t0) cc_final: 0.8436 (t0) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1680 time to fit residues: 13.6075 Evaluate side-chains 41 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 98 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 145 GLN ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.051157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.040268 restraints weight = 66646.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.041189 restraints weight = 42210.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.041831 restraints weight = 29866.716| |-----------------------------------------------------------------------------| r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8605 Z= 0.323 Angle : 0.636 10.919 12170 Z= 0.317 Chirality : 0.039 0.158 1463 Planarity : 0.005 0.061 1272 Dihedral : 18.947 89.716 2135 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.94 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % 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: 926 helix: 0.25 (0.28), residues: 352 sheet: -2.24 (0.40), residues: 137 loop : -2.30 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 398 HIS 0.005 0.001 HIS B 235 PHE 0.021 0.002 PHE B 61 TYR 0.032 0.002 TYR B 146 ARG 0.004 0.001 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 MET cc_start: 0.8651 (mtm) cc_final: 0.8394 (mtt) REVERT: B 320 ASP cc_start: 0.8744 (t0) cc_final: 0.8457 (t0) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1912 time to fit residues: 13.4012 Evaluate side-chains 37 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 91 optimal weight: 0.1980 chunk 64 optimal weight: 0.9980 chunk 71 optimal weight: 0.0000 chunk 25 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 chunk 2 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 145 GLN B 208 HIS B 330 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.054389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.043051 restraints weight = 63935.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.044079 restraints weight = 39602.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.044806 restraints weight = 27511.466| |-----------------------------------------------------------------------------| r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8605 Z= 0.133 Angle : 0.531 8.186 12170 Z= 0.251 Chirality : 0.037 0.149 1463 Planarity : 0.004 0.060 1272 Dihedral : 18.474 81.374 2135 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % 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: -1.24 (0.29), residues: 926 helix: 0.88 (0.30), residues: 348 sheet: -1.71 (0.43), residues: 136 loop : -1.98 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 414 HIS 0.002 0.001 HIS A 208 PHE 0.008 0.001 PHE B 130 TYR 0.008 0.001 TYR A 501 ARG 0.003 0.000 ARG B 125 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 MET cc_start: 0.8738 (mtm) cc_final: 0.8311 (mtt) REVERT: B 42 GLU cc_start: 0.9343 (tt0) cc_final: 0.8797 (mm-30) REVERT: B 124 PHE cc_start: 0.9320 (t80) cc_final: 0.9035 (t80) REVERT: B 183 TYR cc_start: 0.8685 (t80) cc_final: 0.8386 (t80) REVERT: B 320 ASP cc_start: 0.8838 (t0) cc_final: 0.8533 (t70) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1759 time to fit residues: 14.5790 Evaluate side-chains 43 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 80 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 GLN ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.052748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.041485 restraints weight = 65385.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.042497 restraints weight = 39728.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.043188 restraints weight = 27350.862| |-----------------------------------------------------------------------------| r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8605 Z= 0.201 Angle : 0.548 9.555 12170 Z= 0.263 Chirality : 0.037 0.147 1463 Planarity : 0.004 0.061 1272 Dihedral : 18.573 85.091 2135 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % 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: -1.13 (0.29), residues: 926 helix: 1.01 (0.30), residues: 349 sheet: -1.60 (0.42), residues: 147 loop : -1.97 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 401 HIS 0.004 0.001 HIS B 235 PHE 0.011 0.001 PHE A 227 TYR 0.023 0.001 TYR B 146 ARG 0.002 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 MET cc_start: 0.8764 (mtm) cc_final: 0.8383 (mtt) REVERT: B 42 GLU cc_start: 0.9314 (tt0) cc_final: 0.8788 (mm-30) REVERT: B 320 ASP cc_start: 0.8754 (t0) cc_final: 0.8426 (t70) REVERT: B 378 GLU cc_start: 0.9343 (mt-10) cc_final: 0.8835 (mt-10) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1544 time to fit residues: 10.8998 Evaluate side-chains 37 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 40 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 0.3980 chunk 13 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 48 optimal weight: 0.0570 overall best weight: 1.4702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.053365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.041934 restraints weight = 65441.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.042954 restraints weight = 39528.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.043666 restraints weight = 27207.805| |-----------------------------------------------------------------------------| r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8605 Z= 0.157 Angle : 0.522 8.463 12170 Z= 0.248 Chirality : 0.037 0.150 1463 Planarity : 0.004 0.060 1272 Dihedral : 18.455 83.115 2135 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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: -0.88 (0.29), residues: 926 helix: 1.17 (0.30), residues: 349 sheet: -1.31 (0.43), residues: 145 loop : -1.84 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 402 HIS 0.002 0.001 HIS B 235 PHE 0.009 0.001 PHE A 227 TYR 0.015 0.001 TYR B 146 ARG 0.003 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 MET cc_start: 0.8807 (mtm) cc_final: 0.8393 (mtt) REVERT: B 42 GLU cc_start: 0.9322 (tt0) cc_final: 0.8845 (mm-30) REVERT: B 184 MET cc_start: 0.8564 (mmp) cc_final: 0.8314 (mmp) REVERT: B 320 ASP cc_start: 0.8726 (t0) cc_final: 0.8398 (t70) REVERT: B 378 GLU cc_start: 0.9329 (mt-10) cc_final: 0.8813 (mt-10) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1575 time to fit residues: 11.7684 Evaluate side-chains 39 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 60 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 46 optimal weight: 0.0170 chunk 43 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.053439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.041977 restraints weight = 65845.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.043032 restraints weight = 39207.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.043751 restraints weight = 26732.899| |-----------------------------------------------------------------------------| r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8605 Z= 0.156 Angle : 0.518 8.035 12170 Z= 0.247 Chirality : 0.037 0.150 1463 Planarity : 0.004 0.061 1272 Dihedral : 18.423 83.499 2135 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: -0.75 (0.29), residues: 926 helix: 1.25 (0.30), residues: 351 sheet: -1.13 (0.43), residues: 145 loop : -1.80 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 402 HIS 0.002 0.001 HIS B 235 PHE 0.013 0.001 PHE A 160 TYR 0.014 0.001 TYR B 146 ARG 0.003 0.000 ARG B 199 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 TYR cc_start: 0.9298 (m-10) cc_final: 0.8748 (m-80) REVERT: A 171 PHE cc_start: 0.9090 (t80) cc_final: 0.8797 (t80) REVERT: B 41 MET cc_start: 0.8819 (mtm) cc_final: 0.8378 (mtt) REVERT: B 42 GLU cc_start: 0.9308 (tt0) cc_final: 0.8860 (mm-30) REVERT: B 184 MET cc_start: 0.8625 (mmp) cc_final: 0.8396 (mmp) REVERT: B 320 ASP cc_start: 0.8760 (t0) cc_final: 0.8421 (t70) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.2068 time to fit residues: 14.2070 Evaluate side-chains 38 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 8 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 48 optimal weight: 0.0030 chunk 7 optimal weight: 0.0010 chunk 35 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 81 optimal weight: 0.3980 chunk 25 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.054900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.043496 restraints weight = 63841.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.044544 restraints weight = 38675.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.045286 restraints weight = 26606.203| |-----------------------------------------------------------------------------| r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8605 Z= 0.121 Angle : 0.511 8.161 12170 Z= 0.239 Chirality : 0.037 0.149 1463 Planarity : 0.004 0.060 1272 Dihedral : 18.244 80.643 2135 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: -0.60 (0.29), residues: 926 helix: 1.36 (0.30), residues: 350 sheet: -1.00 (0.43), residues: 146 loop : -1.71 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 398 HIS 0.002 0.001 HIS B 208 PHE 0.007 0.001 PHE A 227 TYR 0.008 0.001 TYR A 501 ARG 0.003 0.000 ARG B 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1852 Ramachandran restraints generated. 926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 TYR cc_start: 0.9120 (m-10) cc_final: 0.8760 (m-80) REVERT: A 171 PHE cc_start: 0.8993 (t80) cc_final: 0.8706 (t80) REVERT: B 41 MET cc_start: 0.8823 (mtm) cc_final: 0.8355 (mtt) REVERT: B 42 GLU cc_start: 0.9295 (tt0) cc_final: 0.8847 (mm-30) REVERT: B 53 GLU cc_start: 0.9192 (mp0) cc_final: 0.8983 (pm20) REVERT: B 320 ASP cc_start: 0.8807 (t0) cc_final: 0.8508 (t70) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1513 time to fit residues: 11.6782 Evaluate side-chains 42 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 51 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 16 optimal weight: 0.0980 chunk 5 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.053053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.041785 restraints weight = 65635.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.042810 restraints weight = 39240.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.043525 restraints weight = 26866.569| |-----------------------------------------------------------------------------| r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.5286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8605 Z= 0.185 Angle : 0.522 9.931 12170 Z= 0.249 Chirality : 0.037 0.147 1463 Planarity : 0.004 0.061 1272 Dihedral : 18.407 84.585 2135 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -0.58 (0.29), residues: 926 helix: 1.38 (0.30), residues: 351 sheet: -1.02 (0.43), residues: 148 loop : -1.69 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 414 HIS 0.003 0.001 HIS B 235 PHE 0.010 0.001 PHE A 227 TYR 0.014 0.001 TYR B 146 ARG 0.004 0.000 ARG B 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2110.82 seconds wall clock time: 38 minutes 58.23 seconds (2338.23 seconds total)