Starting phenix.real_space_refine on Fri Sep 11 08:52:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wb2_21585/09_2026/6wb2_21585.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wb2_21585/09_2026/6wb2_21585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wb2_21585/09_2026/6wb2_21585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wb2_21585/09_2026/6wb2_21585.map" model { file = "/net/cci-nas-00/data/ceres_data/6wb2_21585/09_2026/6wb2_21585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wb2_21585/09_2026/6wb2_21585.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6wb2_21585/09_2026/6wb2_21585.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wb2_21585/09_2026/6wb2_21585.cif" } resolution = 4.5 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 9 5.16 5 C 5150 2.51 5 N 1465 2.21 5 O 1711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 8407 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: 3854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 3854 Classifications: {'peptide': 540} Incomplete info: {'truncation_to_alanine': 154} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 504} Chain breaks: 3 Unresolved non-hydrogen bonds: 543 Unresolved non-hydrogen angles: 669 Unresolved non-hydrogen dihedrals: 429 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLU:plan': 33, 'PHE:plan': 2, 'ASP:plan': 10, 'GLN:plan1': 10, 'TYR:plan': 2, 'ASN:plan1': 8, 'ARG:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 287 Chain: "B" Number of atoms: 2968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 2968 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 30, 'TRANS': 375} Chain breaks: 2 Unresolved non-hydrogen bonds: 389 Unresolved non-hydrogen angles: 471 Unresolved non-hydrogen dihedrals: 313 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLU:plan': 29, 'ASP:plan': 12, 'GLN:plan1': 7, 'TYR:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 210 Time building chain proxies: 1.78, per 1000 atoms: 0.21 Number of scatterers: 8407 At special positions: 0 Unit cell: (100.7, 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 9 16.00 P 72 15.00 O 1711 8.00 N 1465 7.00 C 5150 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: 0.81 Conformation dependent library (CDL) restraints added in 277.0 milliseconds 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1780 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 38.7% alpha, 11.4% beta 37 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 removed outlier: 3.787A pdb=" N LEU A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY A 45 " --> pdb=" O MET A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.684A pdb=" N ARG A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.643A pdb=" N LEU A 100 " --> pdb=" O PRO A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.666A pdb=" N PHE A 116 " --> pdb=" O ASP A 113 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 118 " --> pdb=" O TYR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.749A pdb=" N LYS A 126 " --> pdb=" O ASP A 123 " (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 Processing helix chain 'A' and resid 253 through 269 removed outlier: 3.533A pdb=" N GLN A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 283 Processing helix chain 'A' and resid 297 through 311 Processing helix chain 'A' and resid 363 through 383 Processing helix chain 'A' and resid 394 through 404 Processing helix chain 'A' and resid 473 through 488 removed outlier: 3.534A pdb=" N ASP A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 509 removed outlier: 3.582A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN A 509 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 527 removed outlier: 3.763A pdb=" N ASN A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 553 Processing helix chain 'B' and resid 27 through 44 removed outlier: 3.695A pdb=" N ALA B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 91 removed outlier: 6.140A pdb=" N ASP B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N PHE B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TRP B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 103 removed outlier: 3.557A pdb=" N LYS B 103 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 121 through 128 removed outlier: 4.657A pdb=" N LYS B 126 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.775A pdb=" N ASN B 137 " --> pdb=" O SER B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 173 removed outlier: 3.720A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 194 through 211 Processing helix chain 'B' and resid 253 through 268 Processing helix chain 'B' and resid 278 through 283 removed outlier: 4.001A pdb=" N LEU B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 278 through 283' Processing helix chain 'B' and resid 296 through 311 Processing helix chain 'B' and resid 364 through 383 removed outlier: 3.979A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 removed outlier: 3.513A pdb=" N TRP B 398 " --> pdb=" O GLN B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 426 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 60 through 63 removed outlier: 3.620A pdb=" N ARG A 72 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 107 Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 229 Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 351 removed outlier: 7.312A pdb=" N LYS A 347 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN A 343 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE A 341 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N THR A 351 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR A 339 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLN A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE A 329 " --> pdb=" O LYS A 390 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.556A pdb=" N THR A 362 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 512 " --> pdb=" O THR A 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 454 through 455 Processing sheet with id=AA8, first strand: chain 'A' and resid 492 through 497 removed outlier: 4.133A pdb=" N VAL A 493 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR A 532 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR A 497 " --> pdb=" O ALA A 534 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 48 Processing sheet with id=AB1, first strand: chain 'B' and resid 60 through 62 removed outlier: 3.710A pdb=" N PHE B 61 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 74 " --> pdb=" O PHE B 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 179 through 181 removed outlier: 3.586A pdb=" N VAL B 189 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR B 107 " --> pdb=" O VAL B 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 131 through 132 removed outlier: 3.797A pdb=" N ILE B 132 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE B 142 " --> pdb=" O ILE B 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 347 through 354 removed outlier: 7.378A pdb=" N LYS B 347 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN B 343 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE B 341 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N THR B 351 " --> pdb=" O TYR B 339 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N TYR B 339 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LYS B 353 " --> pdb=" O TRP B 337 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N TRP B 337 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS B 390 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) 277 hydrogen bonds defined for protein. 762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 97 hydrogen bonds 186 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 1.21 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2109 1.33 - 1.45: 2037 1.45 - 1.57: 4484 1.57 - 1.69: 143 1.69 - 1.80: 16 Bond restraints: 8789 Sorted by residual: bond pdb=" C1' DC D 77 " pdb=" N1 DC D 77 " ideal model delta sigma weight residual 1.468 1.495 -0.027 1.40e-02 5.10e+03 3.75e+00 bond pdb=" C1' DT D 78 " pdb=" N1 DT D 78 " ideal model delta sigma weight residual 1.468 1.494 -0.026 1.40e-02 5.10e+03 3.47e+00 bond pdb=" N3 DG D 73 " pdb=" C4 DG D 73 " ideal model delta sigma weight residual 1.350 1.362 -0.012 7.00e-03 2.04e+04 3.14e+00 bond pdb=" C5' DG D 73 " pdb=" C4' DG D 73 " ideal model delta sigma weight residual 1.512 1.523 -0.011 7.00e-03 2.04e+04 2.38e+00 bond pdb=" C2 DG D 73 " pdb=" N3 DG D 73 " ideal model delta sigma weight residual 1.323 1.334 -0.011 8.00e-03 1.56e+04 1.76e+00 ... (remaining 8784 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 12100 1.62 - 3.25: 285 3.25 - 4.87: 9 4.87 - 6.49: 3 6.49 - 8.12: 1 Bond angle restraints: 12398 Sorted by residual: angle pdb=" N3 DT D 78 " pdb=" C4 DT D 78 " pdb=" O4 DT D 78 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" O4 DT D 78 " pdb=" C4 DT D 78 " pdb=" C5 DT D 78 " ideal model delta sigma weight residual 124.90 122.28 2.62 7.00e-01 2.04e+00 1.41e+01 angle pdb=" O4' DT D 78 " pdb=" C4' DT D 78 " pdb=" C3' DT D 78 " ideal model delta sigma weight residual 106.00 104.57 1.43 6.00e-01 2.78e+00 5.64e+00 angle pdb=" CA LEU A 525 " pdb=" CB LEU A 525 " pdb=" CG LEU A 525 " ideal model delta sigma weight residual 116.30 124.42 -8.12 3.50e+00 8.16e-02 5.38e+00 angle pdb=" O4' DC D 77 " pdb=" C4' DC D 77 " pdb=" C3' DC D 77 " ideal model delta sigma weight residual 106.00 104.68 1.32 6.00e-01 2.78e+00 4.81e+00 ... (remaining 12393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 4547 16.57 - 33.13: 264 33.13 - 49.70: 96 49.70 - 66.26: 42 66.26 - 82.83: 3 Dihedral angle restraints: 4952 sinusoidal: 2198 harmonic: 2754 Sorted by residual: dihedral pdb=" O5' C D 68 " pdb=" C5' C D 68 " pdb=" C4' C D 68 " pdb=" C3' C D 68 " ideal model delta sinusoidal sigma weight residual 60.00 117.96 -57.96 3 6.40e+00 2.44e-02 5.19e+01 dihedral pdb=" O5' C D 61 " pdb=" C5' C D 61 " pdb=" C4' C D 61 " pdb=" C3' C D 61 " ideal model delta sinusoidal sigma weight residual 60.00 111.70 -51.70 3 6.40e+00 2.44e-02 4.97e+01 dihedral pdb=" O5' A C 198 " pdb=" C5' A C 198 " pdb=" C4' A C 198 " pdb=" C3' A C 198 " ideal model delta sinusoidal sigma weight residual 180.00 132.86 47.14 3 6.40e+00 2.44e-02 4.64e+01 ... (remaining 4949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1200 0.053 - 0.105: 166 0.105 - 0.158: 37 0.158 - 0.211: 0 0.211 - 0.264: 68 Chirality restraints: 1471 Sorted by residual: chirality pdb=" P C C 179 " pdb=" OP1 C C 179 " pdb=" OP2 C C 179 " pdb=" O5' C C 179 " both_signs ideal model delta sigma weight residual True 2.17 -2.44 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" P G C 178 " pdb=" OP1 G C 178 " pdb=" OP2 G C 178 " pdb=" O5' G C 178 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" P G C 195 " pdb=" OP1 G C 195 " pdb=" OP2 G C 195 " pdb=" O5' G C 195 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 1468 not shown) Planarity restraints: 1302 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 278 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.80e+00 pdb=" C GLN A 278 " 0.038 2.00e-02 2.50e+03 pdb=" O GLN A 278 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU A 279 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 51 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO A 52 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 94 " -0.022 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO A 95 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " -0.019 5.00e-02 4.00e+02 ... (remaining 1299 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2438 2.81 - 3.34: 7343 3.34 - 3.86: 14475 3.86 - 4.38: 15217 4.38 - 4.90: 24135 Nonbonded interactions: 63608 Sorted by model distance: nonbonded pdb=" OG1 THR A 58 " pdb=" O ALA A 129 " model vdw 2.293 3.040 nonbonded pdb=" OG1 THR A 240 " pdb=" O VAL A 314 " model vdw 2.306 3.040 nonbonded pdb=" O GLY A 543 " pdb=" NE2 GLN A 547 " model vdw 2.324 3.120 nonbonded pdb=" OD2 ASP A 320 " pdb=" OG SER A 322 " model vdw 2.326 3.040 nonbonded pdb=" OD1 ASN A 460 " pdb=" N LYS A 461 " model vdw 2.366 3.120 ... (remaining 63603 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: 1.020 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.840 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 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 0.027 8789 Z= 0.115 Angle : 0.545 8.118 12398 Z= 0.263 Chirality : 0.064 0.264 1471 Planarity : 0.004 0.037 1302 Dihedral : 13.194 82.830 3172 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.17 % Allowed : 4.59 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -3.59 (0.23), residues: 932 helix: -1.60 (0.25), residues: 325 sheet: -2.38 (0.46), residues: 104 loop : -3.00 (0.23), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 199 TYR 0.003 0.000 TYR B 115 PHE 0.005 0.000 PHE A 77 TRP 0.012 0.000 TRP A 402 HIS 0.001 0.000 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.11 ( 8789) covalent geometry : angle 0.54477 / 0.26 (12398) hydrogen bonds : bond 0.15318 / 7.94 ( 374) hydrogen bonds : angle 5.71305 / 2.21 ( 948) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8526 (tp30) REVERT: A 399 GLU cc_start: 0.8630 (pp20) cc_final: 0.8363 (tm-30) REVERT: B 24 TRP cc_start: 0.6859 (p90) cc_final: 0.6536 (p90) REVERT: B 31 ILE cc_start: 0.9566 (mt) cc_final: 0.9311 (tp) REVERT: B 116 PHE cc_start: 0.8193 (m-10) cc_final: 0.7976 (m-10) REVERT: B 149 LEU cc_start: 0.8714 (mm) cc_final: 0.8326 (mt) REVERT: B 153 TRP cc_start: 0.8522 (t60) cc_final: 0.8155 (t60) REVERT: B 373 GLN cc_start: 0.9130 (mt0) cc_final: 0.8616 (tm-30) REVERT: B 378 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8132 (mt-10) outliers start: 1 outliers final: 1 residues processed: 106 average time/residue: 0.1199 time to fit residues: 16.6395 Evaluate side-chains 66 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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: 1.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 HIS A 151 GLN A 174 GLN A 487 GLN A 494 ASN A 547 GLN B 57 ASN B 367 GLN B 373 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.063009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.051030 restraints weight = 58109.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.052349 restraints weight = 33625.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.053281 restraints weight = 22920.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.053925 restraints weight = 17344.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.054409 restraints weight = 14166.911| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8789 Z= 0.122 Angle : 0.609 7.909 12398 Z= 0.277 Chirality : 0.047 0.194 1471 Planarity : 0.004 0.049 1302 Dihedral : 12.207 70.130 1861 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.17 % Allowed : 4.25 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -2.43 (0.26), residues: 932 helix: -0.17 (0.29), residues: 331 sheet: -1.95 (0.44), residues: 108 loop : -2.65 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 206 TYR 0.023 0.001 TYR A 441 PHE 0.023 0.002 PHE B 171 TRP 0.012 0.001 TRP A 402 HIS 0.012 0.002 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 8789) covalent geometry : angle 0.60876 / 0.28 (12398) hydrogen bonds : bond 0.03593 / 1.88 ( 374) hydrogen bonds : angle 4.55385 / 1.78 ( 948) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.9318 (mm-30) cc_final: 0.8988 (tp30) REVERT: B 42 GLU cc_start: 0.8804 (tp30) cc_final: 0.8595 (tp30) REVERT: B 149 LEU cc_start: 0.8985 (mm) cc_final: 0.8573 (mt) REVERT: B 153 TRP cc_start: 0.8862 (t60) cc_final: 0.8255 (t60) REVERT: B 373 GLN cc_start: 0.9090 (mt0) cc_final: 0.8646 (tm-30) REVERT: B 378 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8237 (mt-10) outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.0978 time to fit residues: 10.3227 Evaluate side-chains 59 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 2 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN A 367 GLN ** A 447 ASN ** 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 = 0.3225 r_free = 0.3225 target = 0.059129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.047355 restraints weight = 58582.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.048550 restraints weight = 34306.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.049384 restraints weight = 23605.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.049971 restraints weight = 18008.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.050395 restraints weight = 14780.642| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8789 Z= 0.192 Angle : 0.659 6.337 12398 Z= 0.302 Chirality : 0.048 0.183 1471 Planarity : 0.004 0.049 1302 Dihedral : 12.149 75.865 1861 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -1.69 (0.27), residues: 932 helix: 0.71 (0.31), residues: 322 sheet: -1.78 (0.46), residues: 114 loop : -2.31 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 72 TYR 0.022 0.002 TYR B 354 PHE 0.010 0.002 PHE B 116 TRP 0.019 0.002 TRP B 88 HIS 0.006 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 ( 8789) covalent geometry : angle 0.65948 / 0.30 (12398) hydrogen bonds : bond 0.04325 / 2.27 ( 374) hydrogen bonds : angle 4.31399 / 1.67 ( 948) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8696 (tp30) REVERT: B 367 GLN cc_start: 0.9010 (pt0) cc_final: 0.8653 (pm20) REVERT: B 373 GLN cc_start: 0.9252 (mt0) cc_final: 0.8704 (tm-30) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0859 time to fit residues: 7.8009 Evaluate side-chains 39 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 72 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 97 optimal weight: 0.2980 chunk 80 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.059768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.047944 restraints weight = 58278.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.049191 restraints weight = 33557.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.050050 restraints weight = 22832.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.050654 restraints weight = 17319.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.051072 restraints weight = 14161.638| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8789 Z= 0.112 Angle : 0.600 7.100 12398 Z= 0.267 Chirality : 0.046 0.180 1471 Planarity : 0.004 0.041 1302 Dihedral : 12.029 75.312 1861 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -1.41 (0.28), residues: 932 helix: 0.93 (0.31), residues: 325 sheet: -1.33 (0.48), residues: 107 loop : -2.22 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 78 TYR 0.011 0.001 TYR A 188 PHE 0.008 0.001 PHE B 171 TRP 0.015 0.001 TRP B 88 HIS 0.008 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 8789) covalent geometry : angle 0.59961 / 0.27 (12398) hydrogen bonds : bond 0.03409 / 1.79 ( 374) hydrogen bonds : angle 4.10581 / 1.58 ( 948) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.290 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 87 PHE cc_start: 0.8582 (m-10) cc_final: 0.8248 (m-10) REVERT: A 315 HIS cc_start: 0.7429 (m90) cc_final: 0.7036 (m-70) REVERT: A 370 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8787 (tp30) REVERT: A 415 GLU cc_start: 0.8924 (mp0) cc_final: 0.8709 (mp0) REVERT: B 149 LEU cc_start: 0.8954 (mm) cc_final: 0.8689 (mm) REVERT: B 153 TRP cc_start: 0.8962 (t60) cc_final: 0.8165 (t60) REVERT: B 208 HIS cc_start: 0.8821 (m-70) cc_final: 0.8312 (m-70) REVERT: B 367 GLN cc_start: 0.8997 (pt0) cc_final: 0.8606 (pm20) REVERT: B 373 GLN cc_start: 0.9272 (mt0) cc_final: 0.8590 (tm-30) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0843 time to fit residues: 8.1217 Evaluate side-chains 49 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 67 optimal weight: 0.0870 chunk 76 optimal weight: 0.0980 chunk 58 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 overall best weight: 2.0364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN ** A 447 ASN ** 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 = 0.3205 r_free = 0.3205 target = 0.058308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.046712 restraints weight = 58917.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.047929 restraints weight = 33877.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.048794 restraints weight = 23038.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.049389 restraints weight = 17385.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.049818 restraints weight = 14185.936| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8789 Z= 0.149 Angle : 0.629 6.684 12398 Z= 0.282 Chirality : 0.047 0.175 1471 Planarity : 0.004 0.048 1302 Dihedral : 12.071 76.702 1861 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 932 helix: 1.12 (0.31), residues: 328 sheet: -1.28 (0.48), residues: 109 loop : -2.06 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 78 TYR 0.020 0.001 TYR A 183 PHE 0.012 0.001 PHE A 440 TRP 0.013 0.001 TRP B 88 HIS 0.006 0.001 HIS B 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 8789) covalent geometry : angle 0.62887 / 0.28 (12398) hydrogen bonds : bond 0.03708 / 1.95 ( 374) hydrogen bonds : angle 3.99859 / 1.53 ( 948) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.9464 (mmm) cc_final: 0.9217 (tpp) REVERT: B 153 TRP cc_start: 0.8993 (t60) cc_final: 0.8126 (t60) REVERT: B 367 GLN cc_start: 0.9073 (pt0) cc_final: 0.8624 (pm20) REVERT: B 373 GLN cc_start: 0.9260 (mt0) cc_final: 0.8675 (tm-30) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0895 time to fit residues: 7.0760 Evaluate side-chains 39 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 21 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 82 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 46 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.058492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.046763 restraints weight = 57373.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.047996 restraints weight = 33063.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.048857 restraints weight = 22462.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.049460 restraints weight = 17022.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.049800 restraints weight = 13886.643| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8789 Z= 0.120 Angle : 0.600 6.869 12398 Z= 0.266 Chirality : 0.046 0.180 1471 Planarity : 0.004 0.039 1302 Dihedral : 12.025 76.768 1861 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.96 (0.28), residues: 932 helix: 1.27 (0.31), residues: 328 sheet: -1.18 (0.48), residues: 109 loop : -1.93 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 78 TYR 0.020 0.001 TYR A 183 PHE 0.020 0.001 PHE B 171 TRP 0.016 0.001 TRP B 88 HIS 0.010 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 8789) covalent geometry : angle 0.59981 / 0.27 (12398) hydrogen bonds : bond 0.03446 / 1.81 ( 374) hydrogen bonds : angle 3.95976 / 1.51 ( 948) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.276 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: B 153 TRP cc_start: 0.9047 (t60) cc_final: 0.8107 (t60) REVERT: B 171 PHE cc_start: 0.8434 (p90) cc_final: 0.8046 (p90) REVERT: B 208 HIS cc_start: 0.8747 (m-70) cc_final: 0.8325 (m-70) REVERT: B 367 GLN cc_start: 0.9075 (pt0) cc_final: 0.8594 (pm20) REVERT: B 373 GLN cc_start: 0.9262 (mt0) cc_final: 0.8678 (tm-30) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.0789 time to fit residues: 6.7281 Evaluate side-chains 43 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 89 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 75 optimal weight: 0.4980 chunk 55 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 87 optimal weight: 9.9990 chunk 15 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN ** A 447 ASN ** 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 = 0.3228 r_free = 0.3228 target = 0.059203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.047429 restraints weight = 58306.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.048671 restraints weight = 33648.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.049539 restraints weight = 22903.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.050156 restraints weight = 17361.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.050578 restraints weight = 14151.558| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8789 Z= 0.093 Angle : 0.587 7.193 12398 Z= 0.260 Chirality : 0.046 0.178 1471 Planarity : 0.004 0.045 1302 Dihedral : 11.932 76.385 1861 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.78 (0.28), residues: 932 helix: 1.35 (0.31), residues: 328 sheet: -1.06 (0.47), residues: 112 loop : -1.77 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 78 TYR 0.016 0.001 TYR A 183 PHE 0.016 0.001 PHE B 171 TRP 0.019 0.001 TRP A 229 HIS 0.008 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 ( 8789) covalent geometry : angle 0.58679 / 0.26 (12398) hydrogen bonds : bond 0.03194 / 1.67 ( 374) hydrogen bonds : angle 3.87538 / 1.49 ( 948) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.249 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 181 TYR cc_start: 0.7550 (m-10) cc_final: 0.7024 (m-80) REVERT: B 149 LEU cc_start: 0.8922 (mm) cc_final: 0.8613 (mm) REVERT: B 153 TRP cc_start: 0.9006 (t60) cc_final: 0.8056 (t60) REVERT: B 171 PHE cc_start: 0.8408 (p90) cc_final: 0.7971 (p90) REVERT: B 208 HIS cc_start: 0.8654 (m-70) cc_final: 0.8165 (m-70) REVERT: B 367 GLN cc_start: 0.9070 (pt0) cc_final: 0.8597 (pm20) REVERT: B 373 GLN cc_start: 0.9080 (tt0) cc_final: 0.8577 (tm-30) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0751 time to fit residues: 6.5776 Evaluate side-chains 44 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 97 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN ** A 447 ASN ** 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 = 0.3198 r_free = 0.3198 target = 0.057851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.046251 restraints weight = 57017.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.047445 restraints weight = 33364.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.048283 restraints weight = 22926.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.048886 restraints weight = 17460.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.049269 restraints weight = 14264.433| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8789 Z= 0.141 Angle : 0.613 6.948 12398 Z= 0.274 Chirality : 0.046 0.200 1471 Planarity : 0.004 0.042 1302 Dihedral : 12.008 76.056 1861 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.73 (0.28), residues: 932 helix: 1.42 (0.31), residues: 329 sheet: -1.12 (0.46), residues: 111 loop : -1.75 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 143 TYR 0.020 0.001 TYR B 354 PHE 0.014 0.002 PHE B 160 TRP 0.012 0.001 TRP B 88 HIS 0.006 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 8789) covalent geometry : angle 0.61310 / 0.27 (12398) hydrogen bonds : bond 0.03836 / 2.01 ( 374) hydrogen bonds : angle 3.91749 / 1.50 ( 948) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.9474 (mmm) cc_final: 0.9204 (tpp) REVERT: A 181 TYR cc_start: 0.7737 (m-10) cc_final: 0.7207 (m-80) REVERT: B 367 GLN cc_start: 0.9108 (pt0) cc_final: 0.8639 (pm20) REVERT: B 373 GLN cc_start: 0.9160 (tt0) cc_final: 0.8605 (tm-30) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0730 time to fit residues: 5.7210 Evaluate side-chains 41 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 98 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 27 optimal weight: 0.0170 chunk 21 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN ** A 447 ASN ** 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 = 0.3196 r_free = 0.3196 target = 0.057774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.046160 restraints weight = 58896.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.047338 restraints weight = 34596.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.048175 restraints weight = 23835.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.048754 restraints weight = 18207.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.049147 restraints weight = 14937.847| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8789 Z= 0.129 Angle : 0.608 6.900 12398 Z= 0.273 Chirality : 0.046 0.205 1471 Planarity : 0.004 0.046 1302 Dihedral : 12.023 75.856 1861 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.79 (0.28), residues: 932 helix: 1.25 (0.31), residues: 334 sheet: -1.16 (0.46), residues: 112 loop : -1.71 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 78 TYR 0.016 0.001 TYR A 183 PHE 0.006 0.001 PHE A 130 TRP 0.014 0.001 TRP B 88 HIS 0.009 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 8789) covalent geometry : angle 0.60844 / 0.27 (12398) hydrogen bonds : bond 0.03730 / 1.96 ( 374) hydrogen bonds : angle 3.96640 / 1.52 ( 948) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.9452 (mmm) cc_final: 0.9189 (tpp) REVERT: A 181 TYR cc_start: 0.7727 (m-10) cc_final: 0.7179 (m-80) REVERT: B 171 PHE cc_start: 0.8382 (p90) cc_final: 0.7985 (p90) REVERT: B 208 HIS cc_start: 0.8725 (m-70) cc_final: 0.8124 (m-70) REVERT: B 367 GLN cc_start: 0.9123 (pt0) cc_final: 0.8654 (pm20) REVERT: B 373 GLN cc_start: 0.9130 (tt0) cc_final: 0.8603 (tm-30) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0748 time to fit residues: 5.5458 Evaluate side-chains 37 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 67 optimal weight: 5.9990 chunk 11 optimal weight: 0.0270 chunk 43 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 19 optimal weight: 0.3980 chunk 71 optimal weight: 3.9990 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN A 447 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.058621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.046869 restraints weight = 58039.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.048084 restraints weight = 33801.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.048930 restraints weight = 23226.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.049546 restraints weight = 17701.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.049975 restraints weight = 14434.158| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8789 Z= 0.094 Angle : 0.592 7.188 12398 Z= 0.262 Chirality : 0.046 0.192 1471 Planarity : 0.004 0.037 1302 Dihedral : 11.941 75.378 1861 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.59 (0.28), residues: 932 helix: 1.39 (0.31), residues: 328 sheet: -0.89 (0.45), residues: 119 loop : -1.57 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 78 TYR 0.021 0.001 TYR A 183 PHE 0.008 0.001 PHE A 87 TRP 0.017 0.001 TRP B 88 HIS 0.010 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 ( 8789) covalent geometry : angle 0.59229 / 0.26 (12398) hydrogen bonds : bond 0.03407 / 1.77 ( 374) hydrogen bonds : angle 3.86302 / 1.47 ( 948) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ILE cc_start: 0.9014 (pt) cc_final: 0.8748 (mm) REVERT: A 181 TYR cc_start: 0.7620 (m-10) cc_final: 0.7070 (m-80) REVERT: A 520 GLN cc_start: 0.9433 (pt0) cc_final: 0.9142 (pp30) REVERT: B 149 LEU cc_start: 0.8858 (mm) cc_final: 0.8525 (mm) REVERT: B 153 TRP cc_start: 0.9043 (t60) cc_final: 0.7974 (t60) REVERT: B 171 PHE cc_start: 0.8355 (p90) cc_final: 0.7969 (p90) REVERT: B 208 HIS cc_start: 0.8717 (m-70) cc_final: 0.8113 (m-70) REVERT: B 367 GLN cc_start: 0.9097 (pt0) cc_final: 0.8582 (pm20) REVERT: B 373 GLN cc_start: 0.9147 (tt0) cc_final: 0.8583 (tm-30) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0853 time to fit residues: 6.8663 Evaluate side-chains 44 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 100 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 86 optimal weight: 0.0980 chunk 21 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3230 r_free = 0.3230 target = 0.059106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.047363 restraints weight = 58179.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.048587 restraints weight = 33894.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.049448 restraints weight = 23277.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.050063 restraints weight = 17760.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.050467 restraints weight = 14497.104| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8789 Z= 0.091 Angle : 0.591 7.253 12398 Z= 0.262 Chirality : 0.046 0.190 1471 Planarity : 0.004 0.043 1302 Dihedral : 11.864 74.842 1861 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.45 (0.28), residues: 932 helix: 1.48 (0.31), residues: 326 sheet: -0.76 (0.45), residues: 119 loop : -1.48 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 78 TYR 0.023 0.001 TYR A 183 PHE 0.005 0.001 PHE A 440 TRP 0.016 0.001 TRP B 88 HIS 0.009 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.09 ( 8789) covalent geometry : angle 0.59114 / 0.26 (12398) hydrogen bonds : bond 0.03388 / 1.76 ( 374) hydrogen bonds : angle 3.80372 / 1.45 ( 948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1302.94 seconds wall clock time: 23 minutes 19.39 seconds (1399.39 seconds total)