Starting phenix.real_space_refine on Fri Sep 11 08:02:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wb1_21584/09_2026/6wb1_21584.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wb1_21584/09_2026/6wb1_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6wb1_21584/09_2026/6wb1_21584.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wb1_21584/09_2026/6wb1_21584.cif" model { file = "/net/cci-nas-00/data/ceres_data/6wb1_21584/09_2026/6wb1_21584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wb1_21584/09_2026/6wb1_21584.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wb1_21584/09_2026/6wb1_21584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wb1_21584/09_2026/6wb1_21584.map" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'RNAv2': 33} Modifications used: {'rna3p_pur': 19, 'rna3p_pyr': 13} Link IDs: {'rna3p': 32} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 880 Classifications: {'DNA': 4, 'RNAv2': 38} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 21} Link IDs: {'rna3p': 41} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 3 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: {'GLU:plan': 40, 'GLN:plan1': 20, 'ASN:plan1': 6, 'PHE:plan': 5, 'ASP:plan': 16, 'TRP:plan': 1, 'ARG:plan': 6, 'HIS:plan': 3, 'TYR:plan': 1} 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: {'GLU:plan': 27, 'ASP:plan': 11, 'TRP:plan': 1, 'GLN:plan1': 10, 'PHE:plan': 1, 'HIS:plan': 2, 'TYR:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 228 Time building chain proxies: 2.05, per 1000 atoms: 0.25 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: 1.03 Conformation dependent library (CDL) restraints added in 267.7 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: 1.02 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: 1.28 Time building geometry restraints manager: 1.24 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 1.339 1.360 -0.021 8.00e-03 1.56e+04 7.18e+00 bond pdb=" N1 DC D 77 " pdb=" C6 DC D 77 " ideal model delta sigma weight residual 1.367 1.357 0.010 6.00e-03 2.78e+04 2.53e+00 bond pdb=" C2 DT D 78 " pdb=" O2 DT D 78 " ideal model delta sigma weight residual 1.220 1.232 -0.012 8.00e-03 1.56e+04 2.35e+00 bond pdb=" N1 DT D 78 " pdb=" C2 DT D 78 " ideal model delta sigma weight residual 1.376 1.388 -0.012 8.00e-03 1.56e+04 2.19e+00 bond pdb=" C3' DG D 73 " pdb=" O3' DG D 73 " ideal model delta sigma weight residual 1.435 1.416 0.019 1.30e-02 5.92e+03 2.11e+00 ... (remaining 8600 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 11773 1.47 - 2.95: 318 2.95 - 4.42: 65 4.42 - 5.89: 4 5.89 - 7.36: 1 Bond angle restraints: 12161 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=" O4' DG D 79 " pdb=" C4' DG D 79 " pdb=" C3' DG D 79 " ideal model delta sigma weight residual 106.00 103.88 2.12 6.00e-01 2.78e+00 1.24e+01 angle pdb=" O4' DG D 73 " pdb=" C4' DG D 73 " pdb=" C3' DG D 73 " ideal model delta sigma weight residual 106.00 103.93 2.07 6.00e-01 2.78e+00 1.19e+01 angle pdb=" O5' DG D 73 " pdb=" C5' DG D 73 " pdb=" C4' DG D 73 " ideal model delta sigma weight residual 109.40 111.99 -2.59 8.00e-01 1.56e+00 1.05e+01 angle pdb=" O4' DT D 78 " pdb=" C4' DT D 78 " pdb=" C3' DT D 78 " ideal model delta sigma weight residual 106.00 104.19 1.81 6.00e-01 2.78e+00 9.13e+00 ... (remaining 12156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 4417 16.61 - 33.22: 265 33.22 - 49.84: 107 49.84 - 66.45: 53 66.45 - 83.06: 5 Dihedral angle restraints: 4847 sinusoidal: 2094 harmonic: 2753 Sorted by residual: 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 180.00 122.72 57.28 3 6.40e+00 2.44e-02 5.18e+01 dihedral pdb=" O5' G D 6 " pdb=" C5' G D 6 " pdb=" C4' G D 6 " pdb=" C3' G D 6 " ideal model delta sinusoidal sigma weight residual 180.00 126.25 53.75 3 6.40e+00 2.44e-02 5.07e+01 dihedral pdb=" O5' G C 197 " pdb=" C5' G C 197 " pdb=" C4' G C 197 " pdb=" C3' G C 197 " ideal model delta sinusoidal sigma weight residual 180.00 127.93 52.07 3 6.40e+00 2.44e-02 4.99e+01 ... (remaining 4844 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1132 0.052 - 0.103: 207 0.103 - 0.155: 52 0.155 - 0.206: 0 0.206 - 0.258: 72 Chirality restraints: 1463 Sorted by residual: chirality pdb=" C3' DT D 78 " pdb=" C4' DT D 78 " pdb=" O3' DT D 78 " pdb=" C2' DT D 78 " both_signs ideal model delta sigma weight residual False -2.73 -2.47 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" P G D 65 " pdb=" OP1 G D 65 " pdb=" OP2 G D 65 " pdb=" O5' G D 65 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" P A C 177 " pdb=" OP1 A C 177 " pdb=" OP2 A C 177 " pdb=" O5' A C 177 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (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: 1.060 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: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 9.870 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 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= 0.138 Angle : 0.602 7.364 12161 Z= 0.315 Chirality : 0.067 0.258 1463 Planarity : 0.003 0.055 1272 Dihedral : 14.181 83.060 3065 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG B 199 TYR 0.010 0.001 TYR B 354 PHE 0.006 0.001 PHE A 227 TRP 0.012 0.001 TRP A 402 HIS 0.003 0.000 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.14 ( 8605) covalent geometry : angle 0.60153 / 0.31 (12161) hydrogen bonds : bond 0.16206 / 8.45 ( 359) hydrogen bonds : angle 5.71107 / 2.08 ( 897) *********************** 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 : 0.235 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: A 366 LYS cc_start: 0.9720 (tppp) cc_final: 0.9464 (mptt) REVERT: B 42 GLU cc_start: 0.9454 (tt0) cc_final: 0.9173 (tt0) REVERT: B 206 ARG cc_start: 0.9155 (mtp180) cc_final: 0.8940 (ttm170) REVERT: B 307 ARG cc_start: 0.9207 (mtm180) cc_final: 0.8985 (mtt-85) REVERT: B 320 ASP cc_start: 0.8915 (t0) cc_final: 0.8595 (t70) REVERT: B 378 GLU cc_start: 0.9395 (OUTLIER) cc_final: 0.9192 (mt-10) outliers start: 3 outliers final: 0 residues processed: 104 average time/residue: 0.1207 time to fit residues: 16.3347 Evaluate side-chains 54 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 0.4980 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.0670 overall best weight: 1.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 ASN A 475 GLN B 57 ASN B 161 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.059476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.048178 restraints weight = 64390.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.049270 restraints weight = 40457.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.050017 restraints weight = 28224.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.050572 restraints weight = 21399.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.050981 restraints weight = 17202.236| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8605 Z= 0.156 Angle : 0.723 8.968 12161 Z= 0.320 Chirality : 0.050 0.241 1463 Planarity : 0.005 0.060 1272 Dihedral : 13.595 73.574 1857 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.43 % Favored : 95.46 % Rotamer: Outliers : 0.18 % Allowed : 3.10 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.54 (0.26), residues: 926 helix: -0.62 (0.27), residues: 343 sheet: -3.75 (0.33), residues: 143 loop : -3.33 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 211 TYR 0.026 0.002 TYR B 146 PHE 0.013 0.002 PHE A 227 TRP 0.017 0.002 TRP A 402 HIS 0.003 0.001 HIS B 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 ( 8605) covalent geometry : angle 0.72258 / 0.32 (12161) hydrogen bonds : bond 0.06044 / 3.07 ( 359) hydrogen bonds : angle 4.40345 / 1.61 ( 897) *********************** 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 68 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ARG cc_start: 0.9013 (ttm110) cc_final: 0.8563 (tpt90) REVERT: B 41 MET cc_start: 0.8591 (mtm) cc_final: 0.8380 (mtt) REVERT: B 115 TYR cc_start: 0.8618 (m-80) cc_final: 0.8301 (m-80) REVERT: B 320 ASP cc_start: 0.8910 (t0) cc_final: 0.8632 (t70) outliers start: 1 outliers final: 0 residues processed: 68 average time/residue: 0.0854 time to fit residues: 8.4608 Evaluate side-chains 48 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 55 optimal weight: 0.0670 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN A 208 HIS A 447 ASN A 545 ASN B 147 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.054341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.042940 restraints weight = 62049.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.043957 restraints weight = 38384.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.044699 restraints weight = 26798.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.045221 restraints weight = 20288.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.045606 restraints weight = 16359.717| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 8605 Z= 0.251 Angle : 0.787 10.698 12161 Z= 0.359 Chirality : 0.049 0.180 1463 Planarity : 0.006 0.110 1272 Dihedral : 13.681 71.675 1857 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.16 % Favored : 93.74 % Rotamer: Outliers : 0.36 % Allowed : 4.20 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.26), residues: 926 helix: -0.11 (0.28), residues: 347 sheet: -3.20 (0.36), residues: 140 loop : -3.07 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 143 TYR 0.023 0.002 TYR B 146 PHE 0.032 0.004 PHE B 416 TRP 0.019 0.002 TRP B 410 HIS 0.005 0.001 HIS B 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.25 ( 8605) covalent geometry : angle 0.78704 / 0.36 (12161) hydrogen bonds : bond 0.07486 / 3.82 ( 359) hydrogen bonds : angle 4.56116 / 1.68 ( 897) *********************** 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 58 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ARG cc_start: 0.9101 (ttm110) cc_final: 0.8661 (tpt90) REVERT: B 42 GLU cc_start: 0.9371 (tt0) cc_final: 0.8879 (tp30) REVERT: B 115 TYR cc_start: 0.8570 (m-80) cc_final: 0.8318 (m-80) REVERT: B 320 ASP cc_start: 0.8836 (t0) cc_final: 0.8536 (t70) outliers start: 2 outliers final: 0 residues processed: 58 average time/residue: 0.0830 time to fit residues: 7.0463 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 : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 71 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN A 545 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.056359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.045027 restraints weight = 65598.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.046088 restraints weight = 40794.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.046817 restraints weight = 28360.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.047325 restraints weight = 21489.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.047689 restraints weight = 17469.052| |-----------------------------------------------------------------------------| r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8605 Z= 0.122 Angle : 0.690 8.346 12161 Z= 0.297 Chirality : 0.047 0.172 1463 Planarity : 0.004 0.060 1272 Dihedral : 13.425 71.988 1857 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.21 % Favored : 95.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.28), residues: 926 helix: 0.45 (0.29), residues: 344 sheet: -2.80 (0.37), residues: 141 loop : -2.55 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 143 TYR 0.013 0.001 TYR B 146 PHE 0.022 0.002 PHE B 130 TRP 0.016 0.001 TRP B 410 HIS 0.002 0.001 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 8605) covalent geometry : angle 0.68968 / 0.30 (12161) hydrogen bonds : bond 0.05628 / 2.85 ( 359) hydrogen bonds : angle 4.10351 / 1.50 ( 897) *********************** 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 54 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ARG cc_start: 0.9126 (ttm110) cc_final: 0.8592 (tpt90) REVERT: B 41 MET cc_start: 0.8594 (mtm) cc_final: 0.8318 (mtt) REVERT: B 42 GLU cc_start: 0.9283 (tt0) cc_final: 0.8611 (tp30) REVERT: B 320 ASP cc_start: 0.8854 (t0) cc_final: 0.8544 (t70) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0820 time to fit residues: 6.5254 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 : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 54 optimal weight: 0.0770 chunk 44 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 overall best weight: 2.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN B 145 GLN B 330 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.053886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.042422 restraints weight = 66664.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.043479 restraints weight = 40551.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.044221 restraints weight = 27807.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.044741 restraints weight = 20833.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.045144 restraints weight = 16764.284| |-----------------------------------------------------------------------------| r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8605 Z= 0.194 Angle : 0.730 10.386 12161 Z= 0.320 Chirality : 0.047 0.180 1463 Planarity : 0.005 0.067 1272 Dihedral : 13.498 72.196 1857 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.16 % Favored : 93.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.27), residues: 926 helix: 0.38 (0.29), residues: 349 sheet: -2.59 (0.40), residues: 133 loop : -2.49 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 463 TYR 0.016 0.002 TYR B 146 PHE 0.021 0.002 PHE B 130 TRP 0.012 0.002 TRP A 402 HIS 0.002 0.001 HIS B 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 ( 8605) covalent geometry : angle 0.72976 / 0.32 (12161) hydrogen bonds : bond 0.06472 / 3.31 ( 359) hydrogen bonds : angle 4.15028 / 1.52 ( 897) *********************** 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 50 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ARG cc_start: 0.9143 (ttm110) cc_final: 0.8649 (tpt90) REVERT: B 41 MET cc_start: 0.8564 (mtm) cc_final: 0.8232 (mtt) REVERT: B 42 GLU cc_start: 0.9303 (tt0) cc_final: 0.8541 (tp30) REVERT: B 320 ASP cc_start: 0.8840 (t0) cc_final: 0.8506 (t0) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0815 time to fit residues: 6.0784 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 : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 12 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 35 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.053750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.042577 restraints weight = 65283.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.043565 restraints weight = 40533.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.044270 restraints weight = 28255.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.044742 restraints weight = 21443.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.045118 restraints weight = 17475.809| |-----------------------------------------------------------------------------| r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8605 Z= 0.169 Angle : 0.708 9.602 12161 Z= 0.306 Chirality : 0.046 0.191 1463 Planarity : 0.004 0.062 1272 Dihedral : 13.413 72.867 1857 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.29 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.28), residues: 926 helix: 0.57 (0.29), residues: 349 sheet: -2.30 (0.41), residues: 133 loop : -2.38 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 463 TYR 0.011 0.002 TYR B 181 PHE 0.015 0.002 PHE B 416 TRP 0.037 0.001 TRP A 401 HIS 0.003 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 ( 8605) covalent geometry : angle 0.70770 / 0.31 (12161) hydrogen bonds : bond 0.06080 / 3.10 ( 359) hydrogen bonds : angle 4.05631 / 1.49 ( 897) *********************** 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 : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 MET cc_start: 0.8697 (mtm) cc_final: 0.8292 (mtt) REVERT: B 42 GLU cc_start: 0.9316 (tt0) cc_final: 0.8601 (tp30) REVERT: B 320 ASP cc_start: 0.8806 (t0) cc_final: 0.8499 (t0) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0712 time to fit residues: 5.3974 Evaluate side-chains 40 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 67 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.054052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.043084 restraints weight = 66806.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.044062 restraints weight = 42151.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.044744 restraints weight = 29521.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.045223 restraints weight = 22493.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.045585 restraints weight = 18315.578| |-----------------------------------------------------------------------------| r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8605 Z= 0.143 Angle : 0.697 9.216 12161 Z= 0.299 Chirality : 0.046 0.203 1463 Planarity : 0.004 0.061 1272 Dihedral : 13.331 72.229 1857 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.40 % Favored : 94.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.28), residues: 926 helix: 0.69 (0.29), residues: 350 sheet: -2.16 (0.40), residues: 143 loop : -2.21 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 143 TYR 0.010 0.001 TYR A 501 PHE 0.021 0.002 PHE B 130 TRP 0.030 0.002 TRP B 398 HIS 0.002 0.001 HIS B 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 8605) covalent geometry : angle 0.69717 / 0.30 (12161) hydrogen bonds : bond 0.05787 / 2.95 ( 359) hydrogen bonds : angle 3.93018 / 1.45 ( 897) *********************** 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 : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 MET cc_start: 0.8556 (mtm) cc_final: 0.8113 (mtt) REVERT: B 42 GLU cc_start: 0.9447 (tt0) cc_final: 0.9244 (tp30) REVERT: B 124 PHE cc_start: 0.9221 (t80) cc_final: 0.9016 (t80) REVERT: B 320 ASP cc_start: 0.8822 (t0) cc_final: 0.8440 (t0) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0624 time to fit residues: 5.2404 Evaluate side-chains 39 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 24 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 85 optimal weight: 20.0000 chunk 67 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.053241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.041772 restraints weight = 65448.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.042793 restraints weight = 40188.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.043528 restraints weight = 27948.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.044029 restraints weight = 21133.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.044427 restraints weight = 17146.714| |-----------------------------------------------------------------------------| r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8605 Z= 0.153 Angle : 0.704 9.353 12161 Z= 0.303 Chirality : 0.046 0.217 1463 Planarity : 0.004 0.061 1272 Dihedral : 13.291 72.208 1857 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.28), residues: 926 helix: 0.74 (0.29), residues: 350 sheet: -2.10 (0.39), residues: 152 loop : -2.10 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 78 TYR 0.011 0.001 TYR A 188 PHE 0.016 0.002 PHE B 130 TRP 0.021 0.002 TRP B 414 HIS 0.003 0.001 HIS B 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 8605) covalent geometry : angle 0.70384 / 0.30 (12161) hydrogen bonds : bond 0.05825 / 2.97 ( 359) hydrogen bonds : angle 3.95254 / 1.46 ( 897) *********************** 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 45 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 MET cc_start: 0.8533 (mtm) cc_final: 0.8119 (mtt) REVERT: B 42 GLU cc_start: 0.9437 (tt0) cc_final: 0.9208 (tp30) REVERT: B 124 PHE cc_start: 0.9219 (t80) cc_final: 0.9003 (t80) REVERT: B 320 ASP cc_start: 0.8822 (t0) cc_final: 0.8469 (t0) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0608 time to fit residues: 4.6077 Evaluate side-chains 39 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 64 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN B 147 ASN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.053958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.042380 restraints weight = 64294.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.043425 restraints weight = 39414.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.044175 restraints weight = 27446.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.044696 restraints weight = 20695.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.045084 restraints weight = 16756.107| |-----------------------------------------------------------------------------| r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4162 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= 0.116 Angle : 0.687 8.772 12161 Z= 0.291 Chirality : 0.046 0.229 1463 Planarity : 0.004 0.061 1272 Dihedral : 13.165 76.028 1857 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.28), residues: 926 helix: 0.86 (0.29), residues: 350 sheet: -1.85 (0.40), residues: 152 loop : -2.06 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 199 TYR 0.009 0.001 TYR A 501 PHE 0.014 0.001 PHE B 130 TRP 0.017 0.001 TRP B 398 HIS 0.002 0.001 HIS B 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 8605) covalent geometry : angle 0.68668 / 0.29 (12161) hydrogen bonds : bond 0.05232 / 2.66 ( 359) hydrogen bonds : angle 3.90001 / 1.45 ( 897) *********************** 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 50 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 MET cc_start: 0.8547 (mtm) cc_final: 0.8101 (mtt) REVERT: B 42 GLU cc_start: 0.9400 (tt0) cc_final: 0.9150 (tp30) REVERT: B 115 TYR cc_start: 0.8690 (m-80) cc_final: 0.8148 (m-80) REVERT: B 124 PHE cc_start: 0.9230 (t80) cc_final: 0.9012 (t80) REVERT: B 320 ASP cc_start: 0.8809 (t0) cc_final: 0.8494 (t0) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0603 time to fit residues: 5.0038 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 : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 54 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 4 optimal weight: 20.0000 chunk 85 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.053495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.042469 restraints weight = 65433.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.043433 restraints weight = 41037.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.044095 restraints weight = 28733.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.044612 restraints weight = 22158.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.044952 restraints weight = 17935.017| |-----------------------------------------------------------------------------| r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4354 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= 0.137 Angle : 0.690 8.905 12161 Z= 0.293 Chirality : 0.046 0.242 1463 Planarity : 0.004 0.062 1272 Dihedral : 13.149 78.728 1857 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.28), residues: 926 helix: 0.86 (0.29), residues: 351 sheet: -1.69 (0.40), residues: 152 loop : -2.00 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 143 TYR 0.010 0.001 TYR A 188 PHE 0.012 0.002 PHE B 130 TRP 0.012 0.001 TRP B 398 HIS 0.003 0.001 HIS B 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 8605) covalent geometry : angle 0.69018 / 0.29 (12161) hydrogen bonds : bond 0.05479 / 2.79 ( 359) hydrogen bonds : angle 3.92152 / 1.46 ( 897) ********************** 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 46 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 MET cc_start: 0.8624 (mtm) cc_final: 0.8175 (mtt) REVERT: B 42 GLU cc_start: 0.9421 (tt0) cc_final: 0.9118 (tp30) REVERT: B 124 PHE cc_start: 0.9312 (t80) cc_final: 0.9041 (t80) REVERT: B 320 ASP cc_start: 0.8873 (t0) cc_final: 0.8510 (t0) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.0601 time to fit residues: 4.5278 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 : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 88 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 90 optimal weight: 0.0980 chunk 65 optimal weight: 0.0570 chunk 63 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 overall best weight: 1.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN A 509 GLN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.053522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.041734 restraints weight = 63853.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.042795 restraints weight = 39113.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.043540 restraints weight = 27127.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.044092 restraints weight = 20536.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.044475 restraints weight = 16534.743| |-----------------------------------------------------------------------------| r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8605 Z= 0.124 Angle : 0.682 8.913 12161 Z= 0.289 Chirality : 0.046 0.250 1463 Planarity : 0.004 0.061 1272 Dihedral : 13.088 81.084 1857 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.28), residues: 926 helix: 0.94 (0.29), residues: 351 sheet: -1.50 (0.40), residues: 156 loop : -2.01 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 78 TYR 0.010 0.001 TYR A 501 PHE 0.010 0.001 PHE B 130 TRP 0.015 0.001 TRP A 402 HIS 0.002 0.001 HIS B 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 8605) covalent geometry : angle 0.68220 / 0.29 (12161) hydrogen bonds : bond 0.05268 / 2.68 ( 359) hydrogen bonds : angle 3.87632 / 1.44 ( 897) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1235.06 seconds wall clock time: 22 minutes 15.48 seconds (1335.48 seconds total)