Starting phenix.real_space_refine on Thu Jul 2 22:12:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fej_29029/07_2026/8fej_29029.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fej_29029/07_2026/8fej_29029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fej_29029/07_2026/8fej_29029.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fej_29029/07_2026/8fej_29029.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fej_29029/07_2026/8fej_29029.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fej_29029/07_2026/8fej_29029.map" } resolution = 4.64 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= 0.009 sd= 0.098 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 6606 2.51 5 N 1743 2.21 5 O 2061 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10464 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3488 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 15, 'TRANS': 440} Restraints were copied for chains: B, C Time building chain proxies: 2.26, per 1000 atoms: 0.22 Number of scatterers: 10464 At special positions: 0 Unit cell: (105.84, 111.24, 123.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 2061 8.00 N 1743 7.00 C 6606 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 387 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 387 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 387 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 412 " distance=2.03 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: 0.72 Conformation dependent library (CDL) restraints added in 254.2 milliseconds 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2556 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 24 sheets defined 36.8% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 67 through 90 Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 119 through 147 removed outlier: 5.226A pdb=" N GLU A 134 " --> pdb=" O HIS A 130 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASN A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASN A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ALA A 145 " --> pdb=" O ASN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 178 removed outlier: 3.946A pdb=" N ASN A 175 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 209 removed outlier: 3.652A pdb=" N ILE A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 213 removed outlier: 3.923A pdb=" N LEU A 213 " --> pdb=" O GLY A 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 210 through 213' Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 234 through 242 removed outlier: 3.585A pdb=" N LEU A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 255 Processing helix chain 'A' and resid 344 through 352 Processing helix chain 'A' and resid 447 through 473 removed outlier: 3.540A pdb=" N GLN A 463 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 32 Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 67 through 90 Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 92 through 94 No H-bonds generated for 'chain 'B' and resid 92 through 94' Processing helix chain 'B' and resid 119 through 147 removed outlier: 5.227A pdb=" N GLU B 134 " --> pdb=" O HIS B 130 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASN B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASN B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ALA B 145 " --> pdb=" O ASN B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 178 removed outlier: 3.945A pdb=" N ASN B 175 " --> pdb=" O GLY B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 209 removed outlier: 3.652A pdb=" N ILE B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 213 removed outlier: 3.922A pdb=" N LEU B 213 " --> pdb=" O GLY B 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 210 through 213' Processing helix chain 'B' and resid 223 through 230 Processing helix chain 'B' and resid 234 through 242 removed outlier: 3.586A pdb=" N LEU B 238 " --> pdb=" O PHE B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 255 Processing helix chain 'B' and resid 344 through 352 Processing helix chain 'B' and resid 447 through 473 removed outlier: 3.541A pdb=" N GLN B 463 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN B 464 " --> pdb=" O GLN B 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 32 Processing helix chain 'C' and resid 64 through 66 No H-bonds generated for 'chain 'C' and resid 64 through 66' Processing helix chain 'C' and resid 67 through 90 Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 119 through 147 removed outlier: 5.226A pdb=" N GLU C 134 " --> pdb=" O HIS C 130 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASN C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASN C 144 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ALA C 145 " --> pdb=" O ASN C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 178 removed outlier: 3.945A pdb=" N ASN C 175 " --> pdb=" O GLY C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 209 removed outlier: 3.652A pdb=" N ILE C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 213 removed outlier: 3.922A pdb=" N LEU C 213 " --> pdb=" O GLY C 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 210 through 213' Processing helix chain 'C' and resid 223 through 230 Processing helix chain 'C' and resid 234 through 242 removed outlier: 3.585A pdb=" N LEU C 238 " --> pdb=" O PHE C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 255 Processing helix chain 'C' and resid 344 through 352 Processing helix chain 'C' and resid 447 through 473 removed outlier: 3.540A pdb=" N GLN C 463 " --> pdb=" O ASN C 459 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN C 464 " --> pdb=" O GLN C 460 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 39 removed outlier: 6.135A pdb=" N GLU A 290 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR A 38 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 288 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 45 Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.700A pdb=" N ALA A 272 " --> pdb=" O ASP A 263 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASP A 263 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N GLU A 274 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE A 261 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 97 Processing sheet with id=AA5, first strand: chain 'A' and resid 153 through 156 Processing sheet with id=AA6, first strand: chain 'A' and resid 221 through 222 removed outlier: 3.536A pdb=" N ILE A 221 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 296 through 297 Processing sheet with id=AA8, first strand: chain 'A' and resid 405 through 406 removed outlier: 3.890A pdb=" N ALA A 380 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 415 through 417 removed outlier: 7.972A pdb=" N LEU A 421 " --> pdb=" O MET B 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 34 through 39 removed outlier: 6.135A pdb=" N GLU B 290 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR B 38 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL B 288 " --> pdb=" O THR B 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 42 through 45 Processing sheet with id=AB3, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.700A pdb=" N ALA B 272 " --> pdb=" O ASP B 263 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASP B 263 " --> pdb=" O ALA B 272 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLU B 274 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE B 261 " --> pdb=" O GLU B 274 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 153 through 156 Processing sheet with id=AB5, first strand: chain 'B' and resid 221 through 222 removed outlier: 3.536A pdb=" N ILE B 221 " --> pdb=" O GLY B 259 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 296 through 297 Processing sheet with id=AB7, first strand: chain 'B' and resid 405 through 406 removed outlier: 3.891A pdb=" N ALA B 380 " --> pdb=" O SER B 405 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 415 through 417 removed outlier: 7.916A pdb=" N LEU B 421 " --> pdb=" O MET C 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 34 through 39 removed outlier: 6.134A pdb=" N GLU C 290 " --> pdb=" O GLY C 36 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR C 38 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL C 288 " --> pdb=" O THR C 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 42 through 45 Processing sheet with id=AC2, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.701A pdb=" N ALA C 272 " --> pdb=" O ASP C 263 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASP C 263 " --> pdb=" O ALA C 272 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLU C 274 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE C 261 " --> pdb=" O GLU C 274 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 153 through 156 Processing sheet with id=AC4, first strand: chain 'C' and resid 221 through 222 removed outlier: 3.536A pdb=" N ILE C 221 " --> pdb=" O GLY C 259 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 296 through 297 Processing sheet with id=AC6, first strand: chain 'C' and resid 372 through 374 removed outlier: 3.890A pdb=" N ALA C 380 " --> pdb=" O SER C 405 " (cutoff:3.500A) 437 hydrogen bonds defined for protein. 1158 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.43 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3486 1.35 - 1.46: 2114 1.46 - 1.58: 4927 1.58 - 1.70: 0 1.70 - 1.81: 78 Bond restraints: 10605 Sorted by residual: bond pdb=" N VAL C 181 " pdb=" CA VAL C 181 " ideal model delta sigma weight residual 1.459 1.467 -0.008 1.25e-02 6.40e+03 4.28e-01 bond pdb=" N VAL B 181 " pdb=" CA VAL B 181 " ideal model delta sigma weight residual 1.459 1.467 -0.008 1.25e-02 6.40e+03 3.68e-01 bond pdb=" N VAL A 181 " pdb=" CA VAL A 181 " ideal model delta sigma weight residual 1.459 1.466 -0.007 1.25e-02 6.40e+03 3.55e-01 bond pdb=" CG PRO A 216 " pdb=" CD PRO A 216 " ideal model delta sigma weight residual 1.503 1.485 0.018 3.40e-02 8.65e+02 2.67e-01 bond pdb=" CG PRO B 216 " pdb=" CD PRO B 216 " ideal model delta sigma weight residual 1.503 1.485 0.018 3.40e-02 8.65e+02 2.66e-01 ... (remaining 10600 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 14177 1.04 - 2.08: 169 2.08 - 3.12: 48 3.12 - 4.16: 6 4.16 - 5.20: 18 Bond angle restraints: 14418 Sorted by residual: angle pdb=" C PRO B 180 " pdb=" N VAL B 181 " pdb=" CA VAL B 181 " ideal model delta sigma weight residual 121.97 126.16 -4.19 1.80e+00 3.09e-01 5.42e+00 angle pdb=" C PRO C 180 " pdb=" N VAL C 181 " pdb=" CA VAL C 181 " ideal model delta sigma weight residual 121.97 126.15 -4.18 1.80e+00 3.09e-01 5.39e+00 angle pdb=" C PRO A 180 " pdb=" N VAL A 181 " pdb=" CA VAL A 181 " ideal model delta sigma weight residual 121.97 126.15 -4.18 1.80e+00 3.09e-01 5.38e+00 angle pdb=" CA LEU C 455 " pdb=" CB LEU C 455 " pdb=" CG LEU C 455 " ideal model delta sigma weight residual 116.30 121.50 -5.20 3.50e+00 8.16e-02 2.21e+00 angle pdb=" CA LEU B 455 " pdb=" CB LEU B 455 " pdb=" CG LEU B 455 " ideal model delta sigma weight residual 116.30 121.45 -5.15 3.50e+00 8.16e-02 2.16e+00 ... (remaining 14413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.45: 5769 16.45 - 32.90: 561 32.90 - 49.35: 159 49.35 - 65.80: 15 65.80 - 82.25: 12 Dihedral angle restraints: 6516 sinusoidal: 2538 harmonic: 3978 Sorted by residual: dihedral pdb=" CA LYS C 79 " pdb=" CB LYS C 79 " pdb=" CG LYS C 79 " pdb=" CD LYS C 79 " ideal model delta sinusoidal sigma weight residual -60.00 -116.09 56.09 3 1.50e+01 4.44e-03 9.38e+00 dihedral pdb=" CA LYS B 79 " pdb=" CB LYS B 79 " pdb=" CG LYS B 79 " pdb=" CD LYS B 79 " ideal model delta sinusoidal sigma weight residual -60.00 -116.08 56.08 3 1.50e+01 4.44e-03 9.38e+00 dihedral pdb=" CA LYS A 79 " pdb=" CB LYS A 79 " pdb=" CG LYS A 79 " pdb=" CD LYS A 79 " ideal model delta sinusoidal sigma weight residual -60.00 -116.06 56.06 3 1.50e+01 4.44e-03 9.38e+00 ... (remaining 6513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1113 0.025 - 0.050: 359 0.050 - 0.075: 136 0.075 - 0.100: 70 0.100 - 0.125: 77 Chirality restraints: 1755 Sorted by residual: chirality pdb=" CA ILE B 57 " pdb=" N ILE B 57 " pdb=" C ILE B 57 " pdb=" CB ILE B 57 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA ILE B 275 " pdb=" N ILE B 275 " pdb=" C ILE B 275 " pdb=" CB ILE B 275 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA VAL A 444 " pdb=" N VAL A 444 " pdb=" C VAL A 444 " pdb=" CB VAL A 444 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 1752 not shown) Planarity restraints: 1854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 368 " -0.013 5.00e-02 4.00e+02 1.98e-02 6.30e-01 pdb=" N PRO C 369 " 0.034 5.00e-02 4.00e+02 pdb=" CA PRO C 369 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO C 369 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 368 " -0.013 5.00e-02 4.00e+02 1.97e-02 6.22e-01 pdb=" N PRO A 369 " 0.034 5.00e-02 4.00e+02 pdb=" CA PRO A 369 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 369 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 368 " -0.013 5.00e-02 4.00e+02 1.96e-02 6.15e-01 pdb=" N PRO B 369 " 0.034 5.00e-02 4.00e+02 pdb=" CA PRO B 369 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO B 369 " -0.011 5.00e-02 4.00e+02 ... (remaining 1851 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2244 2.78 - 3.31: 9986 3.31 - 3.84: 16675 3.84 - 4.37: 18175 4.37 - 4.90: 31657 Nonbonded interactions: 78737 Sorted by model distance: nonbonded pdb=" NZ LYS A 50 " pdb=" O MET A 241 " model vdw 2.253 3.120 nonbonded pdb=" NZ LYS B 50 " pdb=" O MET B 241 " model vdw 2.253 3.120 nonbonded pdb=" NZ LYS C 50 " pdb=" O MET C 241 " model vdw 2.253 3.120 nonbonded pdb=" ND2 ASN B 233 " pdb=" OE2 GLU B 236 " model vdw 2.288 3.120 nonbonded pdb=" ND2 ASN A 233 " pdb=" OE2 GLU A 236 " model vdw 2.289 3.120 ... (remaining 78732 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set refine NCS operators NCS operators will be refined. 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: 1.010 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.550 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:0.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 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 : 0.001 0.018 10620 Z= 0.065 Angle : 0.367 5.198 14448 Z= 0.189 Chirality : 0.039 0.125 1755 Planarity : 0.002 0.020 1854 Dihedral : 13.974 82.248 3915 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.86 % Favored : 96.92 % Rotamer: Outliers : 4.30 % Allowed : 14.94 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.48 (0.24), residues: 1362 helix: 2.10 (0.26), residues: 444 sheet: 0.30 (0.38), residues: 165 loop : -0.81 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 104 TYR 0.008 0.000 TYR C 270 PHE 0.002 0.000 PHE C 371 TRP 0.002 0.000 TRP B 303 HIS 0.000 0.000 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00118 / 0.06 (10605) covalent geometry : angle 0.36772 / 0.19 (14418) SS BOND : bond 0.00064 / 0.03 ( 15) SS BOND : angle 0.22342 / 0.16 ( 30) hydrogen bonds : bond 0.15393 / 10.76 ( 437) hydrogen bonds : angle 6.22454 / 4.28 ( 1158) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 72 ASP cc_start: 0.9230 (t70) cc_final: 0.8664 (m-30) REVERT: A 157 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8298 (mm-40) REVERT: A 235 ASP cc_start: 0.8292 (m-30) cc_final: 0.8035 (p0) REVERT: A 292 MET cc_start: 0.6645 (pmm) cc_final: 0.6059 (pmm) REVERT: A 343 MET cc_start: 0.6173 (ttm) cc_final: 0.5092 (mtt) REVERT: A 347 LEU cc_start: 0.2258 (OUTLIER) cc_final: 0.1922 (tp) outliers start: 17 outliers final: 2 residues processed: 58 average time/residue: 0.0572 time to fit residues: 4.1697 Evaluate side-chains 24 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN A 337 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.054971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.047518 restraints weight = 56523.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.047741 restraints weight = 52229.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.047911 restraints weight = 49271.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.047963 restraints weight = 47128.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.048028 restraints weight = 46151.377| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10620 Z= 0.129 Angle : 0.565 7.421 14448 Z= 0.288 Chirality : 0.045 0.225 1755 Planarity : 0.004 0.054 1854 Dihedral : 3.143 17.975 1461 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.51 % Allowed : 2.53 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.50 (0.24), residues: 1362 helix: 2.11 (0.25), residues: 444 sheet: 0.23 (0.38), residues: 165 loop : -0.76 (0.24), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG C 232 TYR 0.022 0.002 TYR B 74 PHE 0.013 0.002 PHE B 105 TRP 0.003 0.001 TRP B 303 HIS 0.002 0.001 HIS B 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 (10605) covalent geometry : angle 0.56458 / 0.29 (14418) SS BOND : bond 0.00219 / 0.14 ( 15) SS BOND : angle 0.67410 / 0.43 ( 30) hydrogen bonds : bond 0.03643 / 2.47 ( 437) hydrogen bonds : angle 5.18374 / 3.60 ( 1158) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8833 (t70) cc_final: 0.8127 (m-30) REVERT: C 151 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6776 (mp0) REVERT: C 157 GLN cc_start: 0.8949 (mm-40) cc_final: 0.8704 (mm-40) REVERT: C 230 PHE cc_start: 0.8384 (t80) cc_final: 0.7956 (t80) REVERT: C 343 MET cc_start: 0.5283 (ttm) cc_final: 0.3501 (mtt) outliers start: 2 outliers final: 1 residues processed: 23 average time/residue: 0.0611 time to fit residues: 1.8528 Evaluate side-chains 20 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 35 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.053690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.045762 restraints weight = 57088.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.045762 restraints weight = 54753.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.045762 restraints weight = 54753.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.045762 restraints weight = 54753.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.045762 restraints weight = 54753.259| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 10620 Z= 0.112 Angle : 0.513 8.022 14448 Z= 0.262 Chirality : 0.042 0.157 1755 Planarity : 0.004 0.074 1854 Dihedral : 3.056 11.879 1461 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.62 (0.24), residues: 1362 helix: 2.31 (0.25), residues: 435 sheet: 0.17 (0.39), residues: 165 loop : -0.68 (0.24), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 232 TYR 0.012 0.001 TYR A 74 PHE 0.011 0.002 PHE C 105 TRP 0.003 0.001 TRP B 303 HIS 0.002 0.001 HIS C 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (10605) covalent geometry : angle 0.51347 / 0.26 (14418) SS BOND : bond 0.00116 / 0.07 ( 15) SS BOND : angle 0.47375 / 0.30 ( 30) hydrogen bonds : bond 0.03096 / 2.09 ( 437) hydrogen bonds : angle 4.94380 / 3.45 ( 1158) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 ASP cc_start: 0.9088 (t70) cc_final: 0.8557 (m-30) REVERT: B 110 MET cc_start: 0.8093 (tpt) cc_final: 0.7322 (pmm) REVERT: B 157 GLN cc_start: 0.8872 (mm-40) cc_final: 0.8334 (mm-40) REVERT: B 230 PHE cc_start: 0.8616 (t80) cc_final: 0.8343 (t80) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0378 time to fit residues: 1.1655 Evaluate side-chains 19 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 93 optimal weight: 0.6980 chunk 13 optimal weight: 0.0570 chunk 16 optimal weight: 0.0570 chunk 104 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 1 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 125 optimal weight: 0.0670 chunk 85 optimal weight: 10.0000 overall best weight: 0.3554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.054679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.046938 restraints weight = 56921.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.047098 restraints weight = 54208.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.047101 restraints weight = 51573.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.047109 restraints weight = 51518.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.047109 restraints weight = 51402.470| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10620 Z= 0.088 Angle : 0.494 8.216 14448 Z= 0.244 Chirality : 0.042 0.127 1755 Planarity : 0.004 0.076 1854 Dihedral : 3.039 10.965 1461 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.57 (0.24), residues: 1362 helix: 2.37 (0.26), residues: 438 sheet: 0.16 (0.38), residues: 165 loop : -0.81 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 232 TYR 0.008 0.001 TYR B 74 PHE 0.010 0.001 PHE C 105 TRP 0.003 0.001 TRP B 303 HIS 0.000 0.000 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00176 / 0.09 (10605) covalent geometry : angle 0.49416 / 0.24 (14418) SS BOND : bond 0.00065 / 0.04 ( 15) SS BOND : angle 0.32595 / 0.19 ( 30) hydrogen bonds : bond 0.02648 / 1.81 ( 437) hydrogen bonds : angle 4.76040 / 3.31 ( 1158) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 ASP cc_start: 0.9023 (t70) cc_final: 0.8417 (m-30) REVERT: B 110 MET cc_start: 0.8011 (tpt) cc_final: 0.7348 (pmm) REVERT: B 157 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8336 (mm-40) REVERT: B 230 PHE cc_start: 0.8803 (t80) cc_final: 0.8486 (t80) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0463 time to fit residues: 1.3909 Evaluate side-chains 19 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 44 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 118 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 chunk 83 optimal weight: 0.0000 chunk 98 optimal weight: 0.4980 chunk 30 optimal weight: 0.0870 chunk 101 optimal weight: 0.7980 overall best weight: 0.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.054503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.046754 restraints weight = 57282.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.046930 restraints weight = 54347.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.047003 restraints weight = 52317.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.047004 restraints weight = 50699.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.047124 restraints weight = 50692.815| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 10620 Z= 0.079 Angle : 0.460 6.872 14448 Z= 0.226 Chirality : 0.041 0.124 1755 Planarity : 0.003 0.056 1854 Dihedral : 3.104 15.229 1461 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.68 (0.24), residues: 1362 helix: 2.47 (0.25), residues: 438 sheet: 0.13 (0.38), residues: 165 loop : -0.71 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 232 TYR 0.007 0.001 TYR A 74 PHE 0.008 0.001 PHE B 475 TRP 0.003 0.001 TRP B 303 HIS 0.000 0.000 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00156 / 0.08 (10605) covalent geometry : angle 0.45986 / 0.23 (14418) SS BOND : bond 0.00066 / 0.04 ( 15) SS BOND : angle 0.29881 / 0.18 ( 30) hydrogen bonds : bond 0.02483 / 1.69 ( 437) hydrogen bonds : angle 4.61331 / 3.21 ( 1158) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 ASP cc_start: 0.8985 (t70) cc_final: 0.8374 (m-30) REVERT: B 110 MET cc_start: 0.7613 (tpt) cc_final: 0.7398 (pmm) REVERT: B 157 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8393 (mm-40) REVERT: B 230 PHE cc_start: 0.8911 (t80) cc_final: 0.8547 (t80) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0552 time to fit residues: 1.5641 Evaluate side-chains 20 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 92 optimal weight: 9.9990 chunk 59 optimal weight: 0.0270 chunk 103 optimal weight: 0.0030 chunk 62 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 127 optimal weight: 0.0470 chunk 10 optimal weight: 0.0050 chunk 109 optimal weight: 0.0980 chunk 14 optimal weight: 0.0030 chunk 87 optimal weight: 0.0980 chunk 128 optimal weight: 6.9990 overall best weight: 0.0170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.054804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.047048 restraints weight = 57131.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.047165 restraints weight = 53754.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.047324 restraints weight = 52098.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.047380 restraints weight = 50638.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.047380 restraints weight = 49517.001| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10620 Z= 0.083 Angle : 0.479 6.590 14448 Z= 0.232 Chirality : 0.041 0.123 1755 Planarity : 0.003 0.039 1854 Dihedral : 3.005 13.068 1461 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.72 (0.24), residues: 1362 helix: 2.51 (0.25), residues: 438 sheet: 0.22 (0.39), residues: 165 loop : -0.71 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 325 TYR 0.014 0.001 TYR A 74 PHE 0.007 0.001 PHE A 475 TRP 0.003 0.001 TRP C 303 HIS 0.000 0.000 HIS C 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00172 / 0.08 (10605) covalent geometry : angle 0.47934 / 0.23 (14418) SS BOND : bond 0.00078 / 0.04 ( 15) SS BOND : angle 0.28810 / 0.17 ( 30) hydrogen bonds : bond 0.02487 / 1.70 ( 437) hydrogen bonds : angle 4.54304 / 3.16 ( 1158) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 ASP cc_start: 0.8965 (t70) cc_final: 0.8364 (m-30) REVERT: B 110 MET cc_start: 0.7735 (tpt) cc_final: 0.7383 (pmm) REVERT: B 157 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8372 (mm-40) REVERT: B 230 PHE cc_start: 0.8874 (t80) cc_final: 0.8539 (t80) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0554 time to fit residues: 1.6524 Evaluate side-chains 20 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 69 optimal weight: 4.9990 chunk 23 optimal weight: 0.0770 chunk 46 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 127 optimal weight: 0.0870 chunk 61 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.053248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.043165 restraints weight = 60189.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.043679 restraints weight = 51158.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.044051 restraints weight = 45303.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.044325 restraints weight = 41474.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.044522 restraints weight = 38811.649| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 10620 Z= 0.077 Angle : 0.480 8.272 14448 Z= 0.231 Chirality : 0.041 0.174 1755 Planarity : 0.002 0.028 1854 Dihedral : 2.997 13.929 1461 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.24), residues: 1362 helix: 2.61 (0.25), residues: 438 sheet: 0.22 (0.39), residues: 165 loop : -0.70 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 232 TYR 0.011 0.001 TYR A 74 PHE 0.006 0.001 PHE B 475 TRP 0.004 0.001 TRP C 303 HIS 0.000 0.000 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00156 / 0.08 (10605) covalent geometry : angle 0.48040 / 0.23 (14418) SS BOND : bond 0.00074 / 0.04 ( 15) SS BOND : angle 0.30662 / 0.18 ( 30) hydrogen bonds : bond 0.02369 / 1.62 ( 437) hydrogen bonds : angle 4.43407 / 3.10 ( 1158) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 ASP cc_start: 0.9415 (t70) cc_final: 0.9077 (m-30) REVERT: B 164 LEU cc_start: 0.8172 (mm) cc_final: 0.7516 (mm) REVERT: B 230 PHE cc_start: 0.9249 (t80) cc_final: 0.9048 (t80) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0642 time to fit residues: 1.9352 Evaluate side-chains 20 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 30 optimal weight: 6.9990 chunk 29 optimal weight: 0.0980 chunk 4 optimal weight: 0.0670 chunk 11 optimal weight: 0.6980 chunk 114 optimal weight: 0.1980 chunk 62 optimal weight: 7.9990 chunk 70 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 61 optimal weight: 0.0030 chunk 17 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 overall best weight: 0.2128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 289 GLN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.053278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.044500 restraints weight = 57710.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.044965 restraints weight = 50221.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.045224 restraints weight = 45074.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.045515 restraints weight = 42108.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.045723 restraints weight = 39471.519| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10620 Z= 0.095 Angle : 0.530 7.840 14448 Z= 0.266 Chirality : 0.042 0.162 1755 Planarity : 0.004 0.081 1854 Dihedral : 3.304 22.462 1461 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.80 (0.24), residues: 1362 helix: 2.56 (0.25), residues: 438 sheet: 0.27 (0.39), residues: 165 loop : -0.66 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 232 TYR 0.009 0.001 TYR C 74 PHE 0.006 0.001 PHE C 475 TRP 0.004 0.001 TRP C 303 HIS 0.000 0.000 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.10 (10605) covalent geometry : angle 0.53045 / 0.27 (14418) SS BOND : bond 0.00072 / 0.04 ( 15) SS BOND : angle 0.30664 / 0.18 ( 30) hydrogen bonds : bond 0.02700 / 1.76 ( 437) hydrogen bonds : angle 4.47398 / 3.14 ( 1158) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.9052 (t70) cc_final: 0.8511 (m-30) REVERT: A 230 PHE cc_start: 0.8965 (t80) cc_final: 0.8626 (t80) REVERT: A 343 MET cc_start: 0.5604 (ttm) cc_final: 0.3900 (mtt) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0504 time to fit residues: 1.6349 Evaluate side-chains 21 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 120 optimal weight: 0.0470 chunk 51 optimal weight: 0.0980 chunk 62 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 chunk 130 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 118 optimal weight: 0.0020 chunk 5 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 overall best weight: 0.3486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 GLN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.053331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.044673 restraints weight = 57139.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.045109 restraints weight = 50002.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.045448 restraints weight = 45188.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.045694 restraints weight = 41735.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.045885 restraints weight = 39333.405| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10620 Z= 0.091 Angle : 0.535 7.651 14448 Z= 0.257 Chirality : 0.042 0.160 1755 Planarity : 0.003 0.056 1854 Dihedral : 3.311 24.008 1461 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.80 (0.24), residues: 1362 helix: 2.52 (0.25), residues: 438 sheet: 0.28 (0.39), residues: 165 loop : -0.63 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 232 TYR 0.008 0.001 TYR B 74 PHE 0.007 0.001 PHE A 230 TRP 0.004 0.001 TRP A 303 HIS 0.000 0.000 HIS C 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.09 (10605) covalent geometry : angle 0.53517 / 0.26 (14418) SS BOND : bond 0.00068 / 0.04 ( 15) SS BOND : angle 0.33444 / 0.21 ( 30) hydrogen bonds : bond 0.02404 / 1.64 ( 437) hydrogen bonds : angle 4.44512 / 3.12 ( 1158) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.098 Fit side-chains revert: symmetry clash REVERT: A 52 MET cc_start: 0.4151 (tpp) cc_final: 0.3938 (tpp) REVERT: A 72 ASP cc_start: 0.9400 (t70) cc_final: 0.8864 (m-30) REVERT: A 230 PHE cc_start: 0.9307 (t80) cc_final: 0.8967 (t80) REVERT: A 343 MET cc_start: 0.6523 (ttm) cc_final: 0.5123 (mtt) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0510 time to fit residues: 1.6851 Evaluate side-chains 21 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 95 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 105 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 79 optimal weight: 0.0270 chunk 8 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 15 optimal weight: 0.0980 chunk 133 optimal weight: 3.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.054944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.043828 restraints weight = 57843.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.044253 restraints weight = 51023.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.044558 restraints weight = 46308.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.044792 restraints weight = 43201.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.044944 restraints weight = 40822.532| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10620 Z= 0.089 Angle : 0.532 7.047 14448 Z= 0.260 Chirality : 0.041 0.155 1755 Planarity : 0.003 0.051 1854 Dihedral : 3.297 24.405 1461 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.84 (0.24), residues: 1362 helix: 2.57 (0.25), residues: 438 sheet: 0.25 (0.39), residues: 165 loop : -0.61 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 232 TYR 0.008 0.001 TYR A 74 PHE 0.007 0.001 PHE C 230 TRP 0.004 0.001 TRP B 303 HIS 0.001 0.000 HIS C 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.09 (10605) covalent geometry : angle 0.53204 / 0.26 (14418) SS BOND : bond 0.00083 / 0.04 ( 15) SS BOND : angle 0.34065 / 0.21 ( 30) hydrogen bonds : bond 0.02407 / 1.63 ( 437) hydrogen bonds : angle 4.40450 / 3.09 ( 1158) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0491 time to fit residues: 1.6465 Evaluate side-chains 17 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 102 optimal weight: 6.9990 chunk 52 optimal weight: 0.0370 chunk 91 optimal weight: 0.0020 chunk 47 optimal weight: 0.4980 chunk 106 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 116 optimal weight: 0.6980 chunk 4 optimal weight: 0.0970 chunk 48 optimal weight: 0.0030 chunk 43 optimal weight: 4.9990 overall best weight: 0.1274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.053300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.044606 restraints weight = 56877.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.045077 restraints weight = 49195.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.045413 restraints weight = 44075.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.045621 restraints weight = 40463.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.045857 restraints weight = 37849.859| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10620 Z= 0.088 Angle : 0.532 9.096 14448 Z= 0.258 Chirality : 0.041 0.155 1755 Planarity : 0.003 0.048 1854 Dihedral : 3.338 24.701 1461 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.63 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.86 (0.24), residues: 1362 helix: 2.57 (0.25), residues: 438 sheet: 0.25 (0.38), residues: 165 loop : -0.57 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 232 TYR 0.007 0.001 TYR C 74 PHE 0.009 0.001 PHE C 230 TRP 0.004 0.001 TRP B 303 HIS 0.000 0.000 HIS C 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00185 / 0.09 (10605) covalent geometry : angle 0.53251 / 0.26 (14418) SS BOND : bond 0.00066 / 0.04 ( 15) SS BOND : angle 0.34221 / 0.21 ( 30) hydrogen bonds : bond 0.02349 / 1.62 ( 437) hydrogen bonds : angle 4.37560 / 3.07 ( 1158) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 990.36 seconds wall clock time: 17 minutes 49.70 seconds (1069.70 seconds total)