Starting phenix.real_space_refine on Sat Aug 23 07:35:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fej_29029/08_2025/8fej_29029.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fej_29029/08_2025/8fej_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_29029/08_2025/8fej_29029.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fej_29029/08_2025/8fej_29029.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fej_29029/08_2025/8fej_29029.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fej_29029/08_2025/8fej_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-2.0-5787/lib/python3.9/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: 2.49, per 1000 atoms: 0.24 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: 0.92 Conformation dependent library (CDL) restraints added in 426.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.38 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: 1.76 Time building geometry restraints manager: 1.22 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: 1.510 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.760 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 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 aren 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 covalent geometry : bond 0.00118 (10605) covalent geometry : angle 0.36772 (14418) SS BOND : bond 0.00064 ( 15) SS BOND : angle 0.22342 ( 30) hydrogen bonds : bond 0.15393 ( 437) hydrogen bonds : angle 6.22454 ( 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 : 0.134 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: 0.6644 (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: 0.0656 time to fit residues: 4.7277 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 : 0.165 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: C 100 ASN C 453 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 = 0.3709 r_free = 0.3709 target = 0.054977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.047517 restraints weight = 56522.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.047739 restraints weight = 52251.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.047796 restraints weight = 49643.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.047953 restraints weight = 48288.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.047953 restraints weight = 46531.925| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2286 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 aren 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 covalent geometry : bond 0.00257 (10605) covalent geometry : angle 0.56458 (14418) SS BOND : bond 0.00219 ( 15) SS BOND : angle 0.67410 ( 30) hydrogen bonds : bond 0.03643 ( 437) hydrogen bonds : angle 5.18374 ( 1158) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 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: 2 poor density : 22 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8842 (t70) cc_final: 0.8135 (m-30) REVERT: C 151 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6776 (mp0) REVERT: C 157 GLN cc_start: 0.8955 (mm-40) cc_final: 0.8706 (mm-40) REVERT: C 230 PHE cc_start: 0.8387 (t80) cc_final: 0.7959 (t80) REVERT: C 343 MET cc_start: 0.5296 (ttm) cc_final: 0.3514 (mtt) outliers start: 2 outliers final: 1 residues processed: 24 average time/residue: 0.0727 time to fit residues: 2.2515 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 : 0.131 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.0030 chunk 83 optimal weight: 7.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3721 r_free = 0.3721 target = 0.055086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.047416 restraints weight = 56890.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.047487 restraints weight = 53497.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.047523 restraints weight = 52294.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.047525 restraints weight = 51588.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.047525 restraints weight = 51559.058| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10620 Z= 0.100 Angle : 0.500 8.028 14448 Z= 0.254 Chirality : 0.042 0.163 1755 Planarity : 0.004 0.075 1854 Dihedral : 2.994 11.453 1461 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % 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 aren not related in a simple way. whole: 0.27 (0.23), residues: 1362 helix: 1.91 (0.25), residues: 435 sheet: 0.03 (0.39), residues: 165 loop : -0.84 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 232 TYR 0.013 0.001 TYR A 74 PHE 0.010 0.002 PHE C 105 TRP 0.003 0.001 TRP C 303 HIS 0.002 0.001 HIS B 24 Details of bonding type rmsd covalent geometry : bond 0.00202 (10605) covalent geometry : angle 0.50014 (14418) SS BOND : bond 0.00089 ( 15) SS BOND : angle 0.42446 ( 30) hydrogen bonds : bond 0.02944 ( 437) hydrogen bonds : angle 4.87419 ( 1158) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 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 : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 ASP cc_start: 0.8993 (t70) cc_final: 0.8373 (m-30) REVERT: B 110 MET cc_start: 0.7978 (tpt) cc_final: 0.7292 (pmm) REVERT: B 157 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8285 (mm-40) REVERT: B 230 PHE cc_start: 0.8654 (t80) cc_final: 0.8356 (t80) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0742 time to fit residues: 2.3002 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 : 0.134 ------------------------------------------------------------------------------- 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: 0.7980 chunk 13 optimal weight: 4.9990 chunk 16 optimal weight: 0.2980 chunk 104 optimal weight: 0.1980 chunk 74 optimal weight: 6.9990 chunk 92 optimal weight: 0.0050 chunk 71 optimal weight: 0.0370 chunk 1 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 overall best weight: 0.2672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3731 r_free = 0.3731 target = 0.055314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.047559 restraints weight = 56660.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.047760 restraints weight = 53647.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.047840 restraints weight = 51122.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.047956 restraints weight = 49638.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.047969 restraints weight = 48576.219| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.2954 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= 0.084 Angle : 0.480 7.850 14448 Z= 0.238 Chirality : 0.041 0.129 1755 Planarity : 0.004 0.080 1854 Dihedral : 3.088 17.127 1461 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.85 % Favored : 94.93 % 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 aren not related in a simple way. whole: -0.25 (0.22), residues: 1362 helix: 1.37 (0.24), residues: 438 sheet: -0.23 (0.39), residues: 165 loop : -1.11 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 232 TYR 0.008 0.001 TYR A 74 PHE 0.008 0.001 PHE A 475 TRP 0.003 0.001 TRP B 303 HIS 0.001 0.000 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00166 (10605) covalent geometry : angle 0.47992 (14418) SS BOND : bond 0.00054 ( 15) SS BOND : angle 0.28435 ( 30) hydrogen bonds : bond 0.02502 ( 437) hydrogen bonds : angle 4.68865 ( 1158) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 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 : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 ASP cc_start: 0.8963 (t70) cc_final: 0.8352 (m-30) REVERT: B 157 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8352 (mm-40) REVERT: B 230 PHE cc_start: 0.8805 (t80) cc_final: 0.8467 (t80) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0748 time to fit residues: 2.1313 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 : 0.129 ------------------------------------------------------------------------------- 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: 8.9990 chunk 124 optimal weight: 0.0970 chunk 50 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 118 optimal weight: 8.9990 chunk 7 optimal weight: 0.2980 chunk 83 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3711 r_free = 0.3711 target = 0.054557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.046891 restraints weight = 57509.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.046891 restraints weight = 53831.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.046891 restraints weight = 53831.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.046891 restraints weight = 53831.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.046891 restraints weight = 53831.441| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10620 Z= 0.077 Angle : 0.457 6.469 14448 Z= 0.225 Chirality : 0.041 0.127 1755 Planarity : 0.003 0.063 1854 Dihedral : 2.951 14.072 1461 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.29 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % 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 aren not related in a simple way. whole: -0.36 (0.22), residues: 1362 helix: 1.38 (0.24), residues: 438 sheet: -0.40 (0.38), residues: 165 loop : -1.22 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 232 TYR 0.014 0.001 TYR A 74 PHE 0.007 0.001 PHE B 105 TRP 0.003 0.001 TRP B 303 HIS 0.000 0.000 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00158 (10605) covalent geometry : angle 0.45746 (14418) SS BOND : bond 0.00079 ( 15) SS BOND : angle 0.30162 ( 30) hydrogen bonds : bond 0.02357 ( 437) hydrogen bonds : angle 4.57335 ( 1158) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 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 : 0.132 Fit side-chains revert: symmetry clash REVERT: B 72 ASP cc_start: 0.9024 (t70) cc_final: 0.8506 (m-30) REVERT: B 157 GLN cc_start: 0.8889 (mm-40) cc_final: 0.8384 (mm-40) REVERT: B 230 PHE cc_start: 0.8884 (t80) cc_final: 0.8624 (t80) REVERT: B 343 MET cc_start: 0.5195 (ttm) cc_final: 0.3290 (mtt) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0737 time to fit residues: 2.0927 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 : 0.123 ------------------------------------------------------------------------------- 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: 0.6980 chunk 59 optimal weight: 0.0000 chunk 103 optimal weight: 0.0570 chunk 62 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 127 optimal weight: 0.0970 chunk 10 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 14 optimal weight: 0.0000 chunk 87 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 overall best weight: 0.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3715 r_free = 0.3715 target = 0.054634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.046943 restraints weight = 57158.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.047087 restraints weight = 54370.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.047229 restraints weight = 51911.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.047304 restraints weight = 50227.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.047315 restraints weight = 49053.045| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.3384 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= 0.083 Angle : 0.462 6.850 14448 Z= 0.227 Chirality : 0.041 0.160 1755 Planarity : 0.003 0.060 1854 Dihedral : 2.915 13.358 1461 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.29 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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 aren not related in a simple way. whole: -0.48 (0.22), residues: 1362 helix: 1.21 (0.24), residues: 438 sheet: -0.39 (0.37), residues: 165 loop : -1.27 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 325 TYR 0.009 0.001 TYR B 74 PHE 0.006 0.001 PHE B 475 TRP 0.003 0.001 TRP A 303 HIS 0.000 0.000 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00173 (10605) covalent geometry : angle 0.46261 (14418) SS BOND : bond 0.00082 ( 15) SS BOND : angle 0.27798 ( 30) hydrogen bonds : bond 0.02343 ( 437) hydrogen bonds : angle 4.48860 ( 1158) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 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 : 0.151 Fit side-chains revert: symmetry clash REVERT: B 72 ASP cc_start: 0.8964 (t70) cc_final: 0.8356 (m-30) REVERT: B 157 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8492 (mm-40) REVERT: B 230 PHE cc_start: 0.8879 (t80) cc_final: 0.8562 (t80) REVERT: B 343 MET cc_start: 0.5299 (ttm) cc_final: 0.3382 (mtt) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0555 time to fit residues: 1.7368 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 : 0.134 ------------------------------------------------------------------------------- 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: 2.9990 chunk 23 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 chunk 127 optimal weight: 0.8980 chunk 61 optimal weight: 0.0670 chunk 47 optimal weight: 0.0010 chunk 95 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 overall best weight: 0.7928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN ** 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 = 0.3664 r_free = 0.3664 target = 0.052950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.042927 restraints weight = 60960.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.043422 restraints weight = 51940.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.043784 restraints weight = 46101.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.044056 restraints weight = 42179.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.044214 restraints weight = 39460.484| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 10620 Z= 0.082 Angle : 0.465 7.365 14448 Z= 0.228 Chirality : 0.041 0.138 1755 Planarity : 0.003 0.037 1854 Dihedral : 2.915 13.512 1461 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.51 % Favored : 94.27 % 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 aren not related in a simple way. whole: -0.44 (0.22), residues: 1362 helix: 1.32 (0.24), residues: 438 sheet: -0.50 (0.37), residues: 165 loop : -1.25 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 325 TYR 0.008 0.001 TYR A 74 PHE 0.006 0.001 PHE C 475 TRP 0.004 0.001 TRP A 303 HIS 0.001 0.000 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00164 (10605) covalent geometry : angle 0.46507 (14418) SS BOND : bond 0.00136 ( 15) SS BOND : angle 0.33813 ( 30) hydrogen bonds : bond 0.02317 ( 437) hydrogen bonds : angle 4.39872 ( 1158) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 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 : 0.141 Fit side-chains revert: symmetry clash REVERT: B 164 LEU cc_start: 0.8210 (mm) cc_final: 0.7638 (mm) REVERT: B 343 MET cc_start: 0.6436 (ttm) cc_final: 0.5646 (mtt) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0582 time to fit residues: 1.7227 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 : 0.143 ------------------------------------------------------------------------------- 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: 3.9990 chunk 29 optimal weight: 20.0000 chunk 4 optimal weight: 0.0070 chunk 11 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 124 optimal weight: 0.0030 chunk 61 optimal weight: 0.0370 chunk 17 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 overall best weight: 0.5688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3646 r_free = 0.3646 target = 0.052867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.044238 restraints weight = 57261.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.044714 restraints weight = 49335.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.044967 restraints weight = 43940.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.045265 restraints weight = 40776.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.045450 restraints weight = 38301.503| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10620 Z= 0.081 Angle : 0.497 7.174 14448 Z= 0.248 Chirality : 0.041 0.164 1755 Planarity : 0.002 0.033 1854 Dihedral : 3.202 24.438 1461 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.17 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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 aren not related in a simple way. whole: -0.37 (0.22), residues: 1362 helix: 1.32 (0.24), residues: 438 sheet: -0.48 (0.37), residues: 165 loop : -1.17 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 171 TYR 0.007 0.001 TYR A 74 PHE 0.011 0.001 PHE A 230 TRP 0.003 0.001 TRP A 303 HIS 0.000 0.000 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00168 (10605) covalent geometry : angle 0.49776 (14418) SS BOND : bond 0.00094 ( 15) SS BOND : angle 0.32593 ( 30) hydrogen bonds : bond 0.02466 ( 437) hydrogen bonds : angle 4.34091 ( 1158) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 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 : 0.254 Fit side-chains revert: symmetry clash REVERT: A 72 ASP cc_start: 0.9431 (t70) cc_final: 0.8982 (m-30) REVERT: A 230 PHE cc_start: 0.9319 (t80) cc_final: 0.8996 (t80) REVERT: A 343 MET cc_start: 0.6412 (ttm) cc_final: 0.5381 (mtt) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0571 time to fit residues: 1.8536 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 : 0.132 ------------------------------------------------------------------------------- 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: 8.9990 chunk 51 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 47 optimal weight: 30.0000 chunk 130 optimal weight: 0.0040 chunk 119 optimal weight: 0.7980 chunk 118 optimal weight: 0.0170 chunk 5 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 105 optimal weight: 0.0370 chunk 6 optimal weight: 0.9990 overall best weight: 0.2708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3696 r_free = 0.3696 target = 0.053380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.045649 restraints weight = 56525.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.045734 restraints weight = 54015.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.045734 restraints weight = 52452.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.045734 restraints weight = 52452.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.045734 restraints weight = 52452.002| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10620 Z= 0.079 Angle : 0.498 8.344 14448 Z= 0.238 Chirality : 0.041 0.144 1755 Planarity : 0.002 0.025 1854 Dihedral : 3.102 21.103 1461 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.73 % Favored : 94.05 % 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 aren not related in a simple way. whole: -0.41 (0.22), residues: 1362 helix: 1.22 (0.24), residues: 438 sheet: -0.50 (0.36), residues: 165 loop : -1.14 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 171 TYR 0.007 0.001 TYR A 74 PHE 0.010 0.001 PHE A 230 TRP 0.002 0.001 TRP B 303 HIS 0.000 0.000 HIS B 130 Details of bonding type rmsd covalent geometry : bond 0.00163 (10605) covalent geometry : angle 0.49793 (14418) SS BOND : bond 0.00075 ( 15) SS BOND : angle 0.39178 ( 30) hydrogen bonds : bond 0.02174 ( 437) hydrogen bonds : angle 4.22029 ( 1158) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 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 : 0.134 Fit side-chains revert: symmetry clash REVERT: B 72 ASP cc_start: 0.9103 (t70) cc_final: 0.8573 (m-30) REVERT: B 230 PHE cc_start: 0.8981 (t80) cc_final: 0.8742 (t80) REVERT: B 343 MET cc_start: 0.5349 (ttm) cc_final: 0.3296 (mtt) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0758 time to fit residues: 2.1659 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 : 0.133 ------------------------------------------------------------------------------- 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: 0.7980 chunk 25 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 21 optimal weight: 0.0020 chunk 79 optimal weight: 0.0030 chunk 8 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 133 optimal weight: 0.0370 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3684 r_free = 0.3684 target = 0.053957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.043953 restraints weight = 60739.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.044481 restraints weight = 50988.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.044747 restraints weight = 44924.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.045100 restraints weight = 41500.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.045101 restraints weight = 38742.118| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3904 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= 0.087 Angle : 0.513 7.746 14448 Z= 0.249 Chirality : 0.042 0.140 1755 Planarity : 0.003 0.060 1854 Dihedral : 3.109 20.407 1461 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.29 % Favored : 94.27 % 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 aren not related in a simple way. whole: -0.43 (0.22), residues: 1362 helix: 1.17 (0.24), residues: 438 sheet: -0.47 (0.37), residues: 162 loop : -1.14 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 232 TYR 0.006 0.001 TYR B 74 PHE 0.010 0.001 PHE A 230 TRP 0.002 0.001 TRP C 303 HIS 0.001 0.000 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00184 (10605) covalent geometry : angle 0.51347 (14418) SS BOND : bond 0.00084 ( 15) SS BOND : angle 0.36765 ( 30) hydrogen bonds : bond 0.02371 ( 437) hydrogen bonds : angle 4.30680 ( 1158) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 908 Ramachandran restraints generated. 454 Oldfield, 0 Emsley, 454 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 : 0.137 Fit side-chains revert: symmetry clash REVERT: B 72 ASP cc_start: 0.9404 (t70) cc_final: 0.9051 (m-30) REVERT: B 164 LEU cc_start: 0.7883 (mm) cc_final: 0.7292 (mm) REVERT: B 343 MET cc_start: 0.6248 (ttm) cc_final: 0.5554 (mtt) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0563 time to fit residues: 1.7649 Evaluate side-chains 18 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.152 ------------------------------------------------------------------------------- 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: 0.8980 chunk 52 optimal weight: 0.0980 chunk 91 optimal weight: 0.0170 chunk 47 optimal weight: 4.9990 chunk 106 optimal weight: 0.0020 chunk 33 optimal weight: 8.9990 chunk 85 optimal weight: 0.0970 chunk 116 optimal weight: 0.0170 chunk 4 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3687 r_free = 0.3687 target = 0.054126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.044132 restraints weight = 59699.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.044627 restraints weight = 50729.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.044967 restraints weight = 44911.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.045240 restraints weight = 41399.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.045402 restraints weight = 38755.963| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3961 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= 0.084 Angle : 0.496 6.969 14448 Z= 0.241 Chirality : 0.041 0.139 1755 Planarity : 0.003 0.045 1854 Dihedral : 3.054 18.469 1461 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.73 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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 aren not related in a simple way. whole: -0.48 (0.22), residues: 1362 helix: 1.11 (0.24), residues: 438 sheet: -0.46 (0.37), residues: 162 loop : -1.17 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 232 TYR 0.006 0.001 TYR B 74 PHE 0.008 0.001 PHE C 230 TRP 0.003 0.001 TRP C 303 HIS 0.001 0.000 HIS C 130 Details of bonding type rmsd covalent geometry : bond 0.00173 (10605) covalent geometry : angle 0.49601 (14418) SS BOND : bond 0.00065 ( 15) SS BOND : angle 0.35393 ( 30) hydrogen bonds : bond 0.02215 ( 437) hydrogen bonds : angle 4.24689 ( 1158) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1144.17 seconds wall clock time: 20 minutes 43.56 seconds (1243.56 seconds total)