Starting phenix.real_space_refine on Fri Dec 8 11:23:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb1_21584/12_2023/6wb1_21584.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb1_21584/12_2023/6wb1_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb1_21584/12_2023/6wb1_21584.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb1_21584/12_2023/6wb1_21584.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb1_21584/12_2023/6wb1_21584.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wb1_21584/12_2023/6wb1_21584.pdb" } 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 Residue "A PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 448": "NH1" <-> "NH2" Residue "A ASP 511": "OD1" <-> "OD2" Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 5.38, per 1000 atoms: 0.65 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.94 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 3.46 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: 2.83 Time building geometry restraints manager: 3.99 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: 100.78 - 107.43: 801 107.43 - 114.09: 5007 114.09 - 120.74: 3227 120.74 - 127.40: 2858 127.40 - 134.05: 277 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: 4587 17.79 - 35.58: 276 35.58 - 53.37: 109 53.37 - 71.16: 74 71.16 - 88.95: 27 Dihedral angle restraints: 5073 sinusoidal: 2320 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 5070 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 2.520 nonbonded pdb=" O ARG A 211 " pdb=" NE ARG A 211 " model vdw 2.224 2.520 nonbonded pdb=" OG SER A 105 " pdb=" OG SER A 191 " model vdw 2.231 2.440 nonbonded pdb=" O ALA A 538 " pdb=" NZ LYS A 540 " model vdw 2.273 2.520 nonbonded pdb=" O TRP A 239 " pdb=" N GLY A 316 " model vdw 2.302 2.520 ... (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 ========== 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: 0.960 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: 3.960 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 29.240 Find NCS groups from input model: 0.390 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.430 ------------------------------------------------------------------------------- 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 : 16.706 88.947 3291 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 fitting. rotamer outliers: 3 poor density : 103 time to evaluate : 0.917 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 outliers start: 3 outliers final: 0 residues processed: 104 average time/residue: 0.2857 time to fit residues: 37.9412 Evaluate side-chains 50 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.850 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0428 ------------------------------------------------------------------------------- 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: 2.9990 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 30 optimal weight: 0.0980 chunk 48 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 A 547 GLN B 57 ASN B 147 ASN B 161 GLN B 255 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1975 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= 0.174 Angle : 0.545 8.605 12170 Z= 0.267 Chirality : 0.038 0.147 1463 Planarity : 0.004 0.063 1272 Dihedral : 17.757 89.071 2083 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.18 % Allowed : 2.55 % Favored : 97.26 % 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: -3.22 (0.26), residues: 926 helix: -0.29 (0.28), residues: 343 sheet: -3.55 (0.36), residues: 130 loop : -3.26 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 402 HIS 0.003 0.001 HIS B 235 PHE 0.011 0.002 PHE B 130 TYR 0.012 0.001 TYR A 501 ARG 0.011 0.001 ARG B 307 *********************** 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 65 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.2258 time to fit residues: 20.2464 Evaluate side-chains 45 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.883 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2548 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= 0.162 Angle : 0.509 9.061 12170 Z= 0.245 Chirality : 0.037 0.139 1463 Planarity : 0.004 0.060 1272 Dihedral : 17.651 87.144 2083 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % 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: -2.31 (0.28), residues: 926 helix: 0.44 (0.29), residues: 342 sheet: -2.96 (0.39), residues: 130 loop : -2.74 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 410 HIS 0.003 0.001 HIS A 208 PHE 0.017 0.002 PHE B 416 TYR 0.011 0.001 TYR A 501 ARG 0.004 0.001 ARG A 211 *********************** 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 fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2337 time to fit residues: 20.1149 Evaluate side-chains 45 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.901 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1553 ------------------------------------------------------------------------------- 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: 2.9990 chunk 47 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 ASN B 145 GLN B 208 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2887 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= 0.131 Angle : 0.487 8.192 12170 Z= 0.232 Chirality : 0.036 0.138 1463 Planarity : 0.004 0.059 1272 Dihedral : 17.513 83.214 2083 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % 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: -1.75 (0.28), residues: 926 helix: 0.79 (0.30), residues: 343 sheet: -2.35 (0.40), residues: 137 loop : -2.41 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 410 HIS 0.004 0.001 HIS A 208 PHE 0.012 0.001 PHE B 130 TYR 0.013 0.001 TYR B 146 ARG 0.015 0.001 ARG B 307 *********************** 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 59 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2188 time to fit residues: 18.0440 Evaluate side-chains 41 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.819 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0234 ------------------------------------------------------------------------------- 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: 1.9990 chunk 1 optimal weight: 9.9990 chunk 72 optimal weight: 0.0370 chunk 40 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 overall best weight: 2.6064 ------------------------------------------------------------------------------- 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: 0.8258 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8605 Z= 0.244 Angle : 0.568 12.914 12170 Z= 0.276 Chirality : 0.037 0.138 1463 Planarity : 0.005 0.109 1272 Dihedral : 17.836 89.721 2083 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % 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: -1.73 (0.27), residues: 926 helix: 0.68 (0.29), residues: 348 sheet: -2.07 (0.41), residues: 130 loop : -2.41 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 410 HIS 0.004 0.001 HIS B 235 PHE 0.016 0.002 PHE B 416 TYR 0.012 0.002 TYR B 183 ARG 0.019 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 52 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1716 time to fit residues: 13.6913 Evaluate side-chains 40 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.790 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0214 ------------------------------------------------------------------------------- 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: 7.9990 chunk 19 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8605 Z= 0.188 Angle : 0.525 10.248 12170 Z= 0.250 Chirality : 0.036 0.142 1463 Planarity : 0.004 0.060 1272 Dihedral : 17.764 84.208 2083 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % 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: -1.33 (0.28), residues: 926 helix: 0.88 (0.29), residues: 353 sheet: -1.70 (0.43), residues: 130 loop : -2.15 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 401 HIS 0.002 0.001 HIS B 235 PHE 0.010 0.002 PHE A 227 TYR 0.019 0.002 TYR A 405 ARG 0.005 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 49 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1784 time to fit residues: 13.5291 Evaluate side-chains 41 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.878 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0958 ------------------------------------------------------------------------------- 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: 4.9990 chunk 55 optimal weight: 8.9990 chunk 71 optimal weight: 0.0170 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 97 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 44 optimal weight: 0.0970 chunk 38 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.8222 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8605 Z= 0.187 Angle : 0.530 10.910 12170 Z= 0.253 Chirality : 0.036 0.141 1463 Planarity : 0.004 0.060 1272 Dihedral : 17.781 83.972 2083 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % 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: -1.23 (0.28), residues: 926 helix: 0.92 (0.29), residues: 353 sheet: -1.56 (0.42), residues: 130 loop : -2.08 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 398 HIS 0.003 0.001 HIS B 235 PHE 0.010 0.001 PHE A 227 TYR 0.017 0.001 TYR B 146 ARG 0.004 0.000 ARG B 143 *********************** 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 48 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1760 time to fit residues: 12.7712 Evaluate side-chains 41 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.809 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 509 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4404 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= 0.148 Angle : 0.509 9.458 12170 Z= 0.240 Chirality : 0.036 0.139 1463 Planarity : 0.004 0.060 1272 Dihedral : 17.701 82.584 2083 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % 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: -0.93 (0.29), residues: 926 helix: 1.11 (0.30), residues: 347 sheet: -1.23 (0.44), residues: 130 loop : -1.88 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 398 HIS 0.002 0.001 HIS B 235 PHE 0.011 0.001 PHE A 160 TYR 0.011 0.001 TYR B 115 ARG 0.004 0.001 ARG B 143 *********************** 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 49 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1808 time to fit residues: 13.7901 Evaluate side-chains 39 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.829 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0584 ------------------------------------------------------------------------------- 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: 5.9990 chunk 93 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8605 Z= 0.245 Angle : 0.566 12.115 12170 Z= 0.275 Chirality : 0.037 0.144 1463 Planarity : 0.005 0.061 1272 Dihedral : 17.953 86.517 2083 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % 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: -1.10 (0.28), residues: 926 helix: 0.98 (0.30), residues: 346 sheet: -1.49 (0.41), residues: 148 loop : -1.91 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 414 HIS 0.005 0.001 HIS B 235 PHE 0.012 0.002 PHE A 227 TYR 0.018 0.002 TYR B 146 ARG 0.009 0.001 ARG A 211 *********************** 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 47 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.2171 time to fit residues: 14.8695 Evaluate side-chains 38 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.930 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0859 ------------------------------------------------------------------------------- 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: 0.9980 chunk 66 optimal weight: 3.9990 chunk 100 optimal weight: 0.0970 chunk 92 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 overall best weight: 1.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8605 Z= 0.156 Angle : 0.523 9.483 12170 Z= 0.248 Chirality : 0.036 0.145 1463 Planarity : 0.004 0.059 1272 Dihedral : 17.792 83.351 2083 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: -0.91 (0.29), residues: 926 helix: 1.09 (0.30), residues: 348 sheet: -1.26 (0.42), residues: 148 loop : -1.81 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 229 HIS 0.002 0.001 HIS B 235 PHE 0.009 0.001 PHE A 227 TYR 0.012 0.001 TYR B 146 ARG 0.003 0.000 ARG B 143 ********************** 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 fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.2117 time to fit residues: 14.6624 Evaluate side-chains 40 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.897 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1454 ------------------------------------------------------------------------------- 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: 4.9990 chunk 11 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 33 optimal weight: 0.1980 chunk 82 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 4 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.052961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.041753 restraints weight = 65220.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.042768 restraints weight = 40075.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.043467 restraints weight = 27745.936| |-----------------------------------------------------------------------------| r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8605 Z= 0.174 Angle : 0.519 9.534 12170 Z= 0.247 Chirality : 0.036 0.147 1463 Planarity : 0.004 0.060 1272 Dihedral : 17.772 84.050 2083 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % 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: -0.81 (0.29), residues: 926 helix: 1.14 (0.30), residues: 347 sheet: -1.10 (0.42), residues: 148 loop : -1.76 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 401 HIS 0.003 0.001 HIS B 235 PHE 0.010 0.001 PHE A 227 TYR 0.013 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: 1519.60 seconds wall clock time: 28 minutes 36.99 seconds (1716.99 seconds total)