Starting phenix.real_space_refine on Sat Dec 28 13:21:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wb1_21584/12_2024/6wb1_21584.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wb1_21584/12_2024/6wb1_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_21584/12_2024/6wb1_21584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wb1_21584/12_2024/6wb1_21584.map" model { file = "/net/cci-nas-00/data/ceres_data/6wb1_21584/12_2024/6wb1_21584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wb1_21584/12_2024/6wb1_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-5532/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: 5.61, per 1000 atoms: 0.68 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: 2.52 Conformation dependent library (CDL) restraints added in 848.6 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: 2.99 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: 2.91 Time building geometry restraints manager: 2.76 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: 1.430 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.530 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.290 ------------------------------------------------------------------------------- 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 : 0.801 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: 0.2759 time to fit residues: 36.8401 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 : 0.809 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 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 : 0.850 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: 0.8892 (ttm110) cc_final: 0.8453 (tpt90) REVERT: B 41 MET cc_start: 0.8560 (mtm) cc_final: 0.8242 (mtt) REVERT: B 42 GLU cc_start: 0.9519 (tt0) cc_final: 0.9289 (tt0) REVERT: B 206 ARG cc_start: 0.9186 (mtp180) cc_final: 0.8948 (ttm170) REVERT: B 320 ASP cc_start: 0.8964 (t0) cc_final: 0.8728 (t70) outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 0.2165 time to fit residues: 21.0256 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 : 0.815 ------------------------------------------------------------------------------- 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: 6.9990 chunk 28 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 447 ASN A 545 ASN B 147 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8605 Z= 0.251 Angle : 0.563 9.703 12170 Z= 0.278 Chirality : 0.038 0.142 1463 Planarity : 0.004 0.059 1272 Dihedral : 18.603 92.852 2135 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.43 % Favored : 95.46 % Rotamer: Outliers : 0.18 % Allowed : 2.74 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.27), residues: 926 helix: 0.33 (0.29), residues: 342 sheet: -3.12 (0.36), residues: 135 loop : -2.83 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 410 HIS 0.004 0.001 HIS B 235 PHE 0.032 0.003 PHE B 416 TYR 0.014 0.002 TYR A 501 ARG 0.008 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 57 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ARG cc_start: 0.9035 (ttm110) cc_final: 0.8602 (tpt90) REVERT: B 41 MET cc_start: 0.8574 (mtm) cc_final: 0.8310 (mtt) REVERT: B 115 TYR cc_start: 0.8685 (m-80) cc_final: 0.8221 (m-80) REVERT: B 320 ASP cc_start: 0.8855 (t0) cc_final: 0.8544 (t0) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.1781 time to fit residues: 15.1446 Evaluate side-chains 45 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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: 1.9990 chunk 47 optimal weight: 0.0010 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 92 optimal weight: 0.4980 chunk 97 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 545 ASN B 208 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3016 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= 0.135 Angle : 0.500 7.752 12170 Z= 0.238 Chirality : 0.037 0.148 1463 Planarity : 0.004 0.062 1272 Dihedral : 18.304 83.171 2135 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % 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: -1.78 (0.28), residues: 926 helix: 0.76 (0.30), residues: 343 sheet: -2.41 (0.40), residues: 129 loop : -2.41 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 410 HIS 0.002 0.001 HIS A 208 PHE 0.013 0.001 PHE B 130 TYR 0.011 0.001 TYR B 146 ARG 0.004 0.000 ARG B 143 *********************** 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 58 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ILE cc_start: 0.8550 (mt) cc_final: 0.8283 (pt) REVERT: A 211 ARG cc_start: 0.9002 (ttm110) cc_final: 0.8552 (tpt90) REVERT: B 41 MET cc_start: 0.8606 (mtm) cc_final: 0.8236 (mtt) REVERT: B 42 GLU cc_start: 0.9462 (tt0) cc_final: 0.9018 (tp30) REVERT: B 115 TYR cc_start: 0.8756 (m-80) cc_final: 0.8337 (m-80) REVERT: B 320 ASP cc_start: 0.8811 (t0) cc_final: 0.8549 (t70) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1872 time to fit residues: 15.8176 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 : 0.771 ------------------------------------------------------------------------------- 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: 0.0010 chunk 1 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 24 optimal weight: 0.0000 chunk 32 optimal weight: 20.0000 overall best weight: 1.3994 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8605 Z= 0.162 Angle : 0.508 9.112 12170 Z= 0.241 Chirality : 0.037 0.137 1463 Planarity : 0.004 0.062 1272 Dihedral : 18.333 84.604 2135 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % 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: -1.38 (0.28), residues: 926 helix: 0.99 (0.30), residues: 345 sheet: -2.08 (0.43), residues: 129 loop : -2.14 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 402 HIS 0.002 0.001 HIS B 235 PHE 0.010 0.001 PHE A 227 TYR 0.010 0.001 TYR B 146 ARG 0.003 0.000 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 54 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ILE cc_start: 0.8650 (mt) cc_final: 0.8414 (pt) REVERT: A 211 ARG cc_start: 0.8985 (ttm110) cc_final: 0.8565 (tpt90) REVERT: B 41 MET cc_start: 0.8683 (mtm) cc_final: 0.8225 (mtt) REVERT: B 42 GLU cc_start: 0.9421 (tt0) cc_final: 0.8843 (tp30) REVERT: B 115 TYR cc_start: 0.8807 (m-80) cc_final: 0.8364 (m-80) REVERT: B 145 GLN cc_start: 0.8596 (tt0) cc_final: 0.8318 (tt0) REVERT: B 320 ASP cc_start: 0.8788 (t0) cc_final: 0.8530 (t70) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2000 time to fit residues: 16.0807 Evaluate side-chains 45 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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: 20.0000 chunk 19 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 137 ASN B 330 GLN ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8605 Z= 0.344 Angle : 0.658 11.099 12170 Z= 0.328 Chirality : 0.039 0.159 1463 Planarity : 0.005 0.062 1272 Dihedral : 18.999 93.791 2135 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % 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: -1.83 (0.27), residues: 926 helix: 0.45 (0.29), residues: 353 sheet: -2.10 (0.40), residues: 142 loop : -2.37 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 426 HIS 0.007 0.001 HIS B 235 PHE 0.031 0.003 PHE B 416 TYR 0.038 0.003 TYR B 146 ARG 0.004 0.001 ARG B 143 *********************** 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 47 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 366 LYS cc_start: 0.9698 (ttpt) cc_final: 0.9256 (ptmt) REVERT: B 41 MET cc_start: 0.8541 (mtm) cc_final: 0.8243 (mtt) REVERT: B 115 TYR cc_start: 0.8904 (m-80) cc_final: 0.8425 (m-80) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1661 time to fit residues: 12.1309 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 : 0.880 ------------------------------------------------------------------------------- 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: 9.9990 chunk 71 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 54 optimal weight: 0.4980 chunk 97 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4583 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= 0.192 Angle : 0.544 8.259 12170 Z= 0.262 Chirality : 0.037 0.144 1463 Planarity : 0.004 0.060 1272 Dihedral : 18.619 83.900 2135 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % 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: -1.34 (0.28), residues: 926 helix: 0.84 (0.30), residues: 355 sheet: -1.79 (0.42), residues: 137 loop : -2.11 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 398 HIS 0.002 0.001 HIS B 235 PHE 0.010 0.001 PHE A 227 TYR 0.011 0.001 TYR B 146 ARG 0.003 0.000 ARG B 125 *********************** 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 51 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 MET cc_start: 0.8667 (mtm) cc_final: 0.8303 (mtt) REVERT: B 115 TYR cc_start: 0.8935 (m-80) cc_final: 0.8398 (m-80) REVERT: B 145 GLN cc_start: 0.8911 (tt0) cc_final: 0.8638 (tt0) REVERT: B 320 ASP cc_start: 0.8691 (t0) cc_final: 0.8320 (t0) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1663 time to fit residues: 13.1805 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 : 0.816 ------------------------------------------------------------------------------- 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: 8.9990 chunk 19 optimal weight: 0.4980 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 88 optimal weight: 0.0980 chunk 93 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4627 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= 0.130 Angle : 0.513 8.092 12170 Z= 0.241 Chirality : 0.037 0.144 1463 Planarity : 0.004 0.060 1272 Dihedral : 18.332 81.188 2135 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % 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: -0.85 (0.29), residues: 926 helix: 1.26 (0.30), residues: 342 sheet: -1.46 (0.42), residues: 146 loop : -1.77 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 398 HIS 0.001 0.000 HIS A 208 PHE 0.009 0.001 PHE B 416 TYR 0.016 0.001 TYR B 146 ARG 0.003 0.000 ARG B 125 *********************** 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 51 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 PHE cc_start: 0.9042 (t80) cc_final: 0.8701 (t80) REVERT: B 41 MET cc_start: 0.8699 (mtm) cc_final: 0.8273 (mtt) REVERT: B 42 GLU cc_start: 0.9361 (tt0) cc_final: 0.8961 (mm-30) REVERT: B 115 TYR cc_start: 0.8912 (m-80) cc_final: 0.8361 (m-80) REVERT: B 145 GLN cc_start: 0.8858 (tt0) cc_final: 0.8410 (tm-30) REVERT: B 183 TYR cc_start: 0.8543 (t80) cc_final: 0.8235 (t80) REVERT: B 184 MET cc_start: 0.8451 (mmp) cc_final: 0.7968 (mmm) REVERT: B 320 ASP cc_start: 0.8787 (t0) cc_final: 0.8523 (t70) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1620 time to fit residues: 13.1271 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 : 0.757 ------------------------------------------------------------------------------- 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: 0.7980 chunk 93 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8605 Z= 0.144 Angle : 0.506 8.133 12170 Z= 0.238 Chirality : 0.036 0.149 1463 Planarity : 0.004 0.060 1272 Dihedral : 18.335 83.132 2135 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % 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: -0.72 (0.29), residues: 926 helix: 1.30 (0.30), residues: 348 sheet: -1.27 (0.42), residues: 146 loop : -1.72 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 398 HIS 0.002 0.001 HIS B 235 PHE 0.009 0.001 PHE A 227 TYR 0.009 0.001 TYR A 501 ARG 0.002 0.000 ARG B 125 *********************** 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 49 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 MET cc_start: 0.8701 (mtm) cc_final: 0.8271 (mtt) REVERT: B 42 GLU cc_start: 0.9359 (tt0) cc_final: 0.8925 (mm-30) REVERT: B 115 TYR cc_start: 0.8921 (m-80) cc_final: 0.8391 (m-80) REVERT: B 183 TYR cc_start: 0.8612 (t80) cc_final: 0.8377 (t80) REVERT: B 184 MET cc_start: 0.8572 (mmp) cc_final: 0.8209 (mmm) REVERT: B 320 ASP cc_start: 0.8796 (t0) cc_final: 0.8520 (t70) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1545 time to fit residues: 12.1660 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 : 0.812 ------------------------------------------------------------------------------- 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: 3.9990 chunk 66 optimal weight: 4.9990 chunk 100 optimal weight: 0.2980 chunk 92 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 63 optimal weight: 0.2980 chunk 85 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8605 Z= 0.150 Angle : 0.515 8.051 12170 Z= 0.244 Chirality : 0.036 0.141 1463 Planarity : 0.004 0.060 1272 Dihedral : 18.330 82.991 2135 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % 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: -0.54 (0.29), residues: 926 helix: 1.41 (0.30), residues: 344 sheet: -1.07 (0.42), residues: 146 loop : -1.58 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 402 HIS 0.002 0.001 HIS B 235 PHE 0.010 0.001 PHE A 227 TYR 0.014 0.001 TYR B 146 ARG 0.006 0.001 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 47 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 PHE cc_start: 0.9034 (t80) cc_final: 0.8716 (t80) REVERT: B 41 MET cc_start: 0.8652 (mtm) cc_final: 0.8253 (mtt) REVERT: B 42 GLU cc_start: 0.9343 (tt0) cc_final: 0.8966 (mm-30) REVERT: B 115 TYR cc_start: 0.8947 (m-80) cc_final: 0.8376 (m-80) REVERT: B 184 MET cc_start: 0.8594 (mmp) cc_final: 0.8247 (mmm) REVERT: B 320 ASP cc_start: 0.8788 (t0) cc_final: 0.8515 (t70) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1881 time to fit residues: 13.5235 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 : 1.040 ------------------------------------------------------------------------------- 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: 0.0970 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 overall best weight: 1.3180 ------------------------------------------------------------------------------- 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 = 0.3066 r_free = 0.3066 target = 0.053665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.042247 restraints weight = 64500.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.043294 restraints weight = 38816.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.044027 restraints weight = 26636.773| |-----------------------------------------------------------------------------| r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.5080 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= 0.150 Angle : 0.509 8.676 12170 Z= 0.240 Chirality : 0.036 0.143 1463 Planarity : 0.004 0.060 1272 Dihedral : 18.329 83.205 2135 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % 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: -0.64 (0.29), residues: 926 helix: 1.20 (0.30), residues: 357 sheet: -0.97 (0.43), residues: 146 loop : -1.67 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 402 HIS 0.002 0.001 HIS B 235 PHE 0.014 0.001 PHE B 416 TYR 0.011 0.001 TYR B 146 ARG 0.004 0.000 ARG A 557 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1571.25 seconds wall clock time: 29 minutes 28.91 seconds (1768.91 seconds total)