Starting phenix.real_space_refine on Tue Mar 3 13:34:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ctg_26989/03_2026/8ctg_26989.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ctg_26989/03_2026/8ctg_26989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ctg_26989/03_2026/8ctg_26989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ctg_26989/03_2026/8ctg_26989.map" model { file = "/net/cci-nas-00/data/ceres_data/8ctg_26989/03_2026/8ctg_26989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ctg_26989/03_2026/8ctg_26989.cif" } resolution = 3.8 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= 0.002 sd= 0.035 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 45 5.16 5 C 3041 2.51 5 N 1006 2.21 5 O 1008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5100 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 618 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 105} Unresolved non-hydrogen bonds: 343 Unresolved non-hydrogen angles: 440 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 7, 'TYR:plan': 6, 'ASN:plan1': 4, 'PHE:plan': 5, 'HIS:plan': 2, 'ASP:plan': 8, 'TRP:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 222 Chain: "B" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 1585 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 241} Link IDs: {'PTRANS': 4, 'TRANS': 311} Unresolved non-hydrogen bonds: 908 Unresolved non-hydrogen angles: 1156 Unresolved non-hydrogen dihedrals: 769 Unresolved non-hydrogen chiralities: 70 Planarities with less than four sites: {'TRP:plan': 8, 'ASN:plan1': 18, 'PHE:plan': 11, 'TYR:plan': 5, 'GLN:plan1': 12, 'GLU:plan': 21, 'ARG:plan': 20, 'HIS:plan': 8, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 541 Chain: "C" Number of atoms: 2880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 2880 Classifications: {'peptide': 572} Incomplete info: {'truncation_to_alanine': 456} Link IDs: {'PTRANS': 24, 'TRANS': 547} Chain breaks: 3 Unresolved non-hydrogen bonds: 1778 Unresolved non-hydrogen angles: 2320 Unresolved non-hydrogen dihedrals: 1490 Unresolved non-hydrogen chiralities: 166 Planarities with less than four sites: {'TYR:plan': 21, 'ASN:plan1': 22, 'ARG:plan': 37, 'ASP:plan': 51, 'GLU:plan': 35, 'PHE:plan': 17, 'HIS:plan': 12, 'TRP:plan': 19, 'GLN:plan1': 15} Unresolved non-hydrogen planarities: 1084 Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PAM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PAM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Residues with excluded nonbonded symmetry interactions: 69 residue: pdb=" N LEU A 97 " occ=0.20 ... (3 atoms not shown) pdb=" CB LEU A 97 " occ=0.20 residue: pdb=" N GLU A 98 " occ=0.20 ... (3 atoms not shown) pdb=" CB GLU A 98 " occ=0.20 residue: pdb=" N ASP A 99 " occ=0.20 ... (3 atoms not shown) pdb=" CB ASP A 99 " occ=0.20 residue: pdb=" N TYR A 100 " occ=0.20 ... (3 atoms not shown) pdb=" CB TYR A 100 " occ=0.20 residue: pdb=" N LYS A 101 " occ=0.20 ... (3 atoms not shown) pdb=" CB LYS A 101 " occ=0.20 residue: pdb=" N PRO B 67 " occ=0.20 ... (5 atoms not shown) pdb=" CD PRO B 67 " occ=0.20 residue: pdb=" N GLU B 68 " occ=0.20 ... (3 atoms not shown) pdb=" CB GLU B 68 " occ=0.20 residue: pdb=" N SER B 69 " occ=0.20 ... (3 atoms not shown) pdb=" CB SER B 69 " occ=0.20 residue: pdb=" N THR B 70 " occ=0.20 ... (3 atoms not shown) pdb=" CB THR B 70 " occ=0.20 residue: pdb=" N LEU B 71 " occ=0.20 ... (3 atoms not shown) pdb=" CB LEU B 71 " occ=0.20 residue: pdb=" N GLN B 72 " occ=0.20 ... (3 atoms not shown) pdb=" CB GLN B 72 " occ=0.20 residue: pdb=" N LEU B 73 " occ=0.20 ... (3 atoms not shown) pdb=" CB LEU B 73 " occ=0.20 ... (remaining 57 not shown) Time building chain proxies: 1.58, per 1000 atoms: 0.31 Number of scatterers: 5100 At special positions: 0 Unit cell: (69.0201, 97.9915, 134.632, 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 45 16.00 O 1008 8.00 N 1006 7.00 C 3041 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 89 " distance=2.03 Simple disulfide: pdb=" SG CYS A 80 " - pdb=" SG CYS A 118 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 135 " distance=2.04 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 66 " distance=2.03 Simple disulfide: pdb=" SG CYS B 105 " - pdb=" SG CYS B 113 " distance=2.03 Simple disulfide: pdb=" SG CYS B 115 " - pdb=" SG CYS B 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 181 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 190 " distance=2.03 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 298 " distance=2.04 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 295 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 328 " distance=2.02 Simple disulfide: pdb=" SG CYS B 315 " - pdb=" SG CYS B 325 " distance=2.03 Simple disulfide: pdb=" SG CYS B 320 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS C 286 " - pdb=" SG CYS C 297 " distance=2.03 Simple disulfide: pdb=" SG CYS C 293 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 310 " - pdb=" SG CYS C 323 " distance=2.03 Simple disulfide: pdb=" SG CYS C 592 " - pdb=" SG CYS C 603 " distance=2.04 Simple disulfide: pdb=" SG CYS C 599 " - pdb=" SG CYS C 612 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 397.4 milliseconds 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1862 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 19 sheets defined 22.1% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 61 through 70 Processing helix chain 'A' and resid 72 through 79 Processing helix chain 'A' and resid 81 through 93 removed outlier: 4.538A pdb=" N LYS A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE A 86 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 125 Proline residue: A 120 - end of helix Processing helix chain 'A' and resid 130 through 134 removed outlier: 3.511A pdb=" N ARG A 134 " --> pdb=" O ASP A 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 59 removed outlier: 3.581A pdb=" N SER B 41 " --> pdb=" O TYR B 37 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N SER B 43 " --> pdb=" O THR B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 76 Processing helix chain 'B' and resid 83 through 107 removed outlier: 3.789A pdb=" N SER B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE B 88 " --> pdb=" O ARG B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 115 removed outlier: 5.995A pdb=" N ASN B 112 " --> pdb=" O ASP B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 152 removed outlier: 3.740A pdb=" N GLY B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 176 Processing helix chain 'B' and resid 185 through 189 Processing helix chain 'B' and resid 201 through 215 removed outlier: 3.521A pdb=" N ILE B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 Processing helix chain 'B' and resid 284 through 295 removed outlier: 4.118A pdb=" N CYS B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LYS B 292 " --> pdb=" O ARG B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 299 Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 289 through 293 Processing helix chain 'C' and resid 590 through 599 removed outlier: 4.417A pdb=" N GLU C 595 " --> pdb=" O CYS C 592 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ASN C 596 " --> pdb=" O ALA C 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 Processing sheet with id=AA2, first strand: chain 'B' and resid 123 through 125 removed outlier: 6.479A pdb=" N ILE B 123 " --> pdb=" O TRP B 130 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TRP B 130 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY B 125 " --> pdb=" O TRP B 128 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 129 " --> pdb=" O CYS B 195 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N LEU B 197 " --> pdb=" O VAL B 129 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 262 through 263 Processing sheet with id=AA4, first strand: chain 'B' and resid 275 through 276 Processing sheet with id=AA5, first strand: chain 'B' and resid 310 through 311 Processing sheet with id=AA6, first strand: chain 'C' and resid 31 through 34 removed outlier: 3.840A pdb=" N ARG C 32 " --> pdb=" O TYR C 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 59 removed outlier: 6.176A pdb=" N SER C 68 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL C 56 " --> pdb=" O TYR C 66 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TYR C 66 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE C 58 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU C 64 " --> pdb=" O PHE C 58 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE C 75 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 97 through 103 removed outlier: 3.647A pdb=" N GLY C 99 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG C 118 " --> pdb=" O ASP C 113 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE C 119 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 140 through 146 removed outlier: 4.665A pdb=" N ALA C 142 " --> pdb=" O THR C 155 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE C 163 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 184 through 190 removed outlier: 5.200A pdb=" N GLY C 186 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA C 199 " --> pdb=" O GLY C 186 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE C 206 " --> pdb=" O GLN C 217 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 230 through 232 removed outlier: 3.669A pdb=" N THR C 231 " --> pdb=" O TYR C 238 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR C 238 " --> pdb=" O THR C 231 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE C 247 " --> pdb=" O ILE C 261 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 296 through 299 Processing sheet with id=AB4, first strand: chain 'C' and resid 351 through 353 removed outlier: 3.539A pdb=" N ILE C 342 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU C 330 " --> pdb=" O THR C 581 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR C 581 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU C 332 " --> pdb=" O LYS C 579 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS C 579 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY C 577 " --> pdb=" O ALA C 334 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 362 through 368 removed outlier: 4.219A pdb=" N ALA C 364 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE C 384 " --> pdb=" O VAL C 397 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 407 through 411 removed outlier: 6.593A pdb=" N ILE C 427 " --> pdb=" O LEU C 440 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 448 through 454 removed outlier: 4.753A pdb=" N ALA C 450 " --> pdb=" O THR C 463 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE C 471 " --> pdb=" O LEU C 484 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 492 through 498 removed outlier: 3.532A pdb=" N GLY C 494 " --> pdb=" O GLY C 507 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS C 513 " --> pdb=" O ASP C 508 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE C 514 " --> pdb=" O LEU C 527 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 539 through 541 removed outlier: 3.657A pdb=" N TYR C 544 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ARG C 557 " --> pdb=" O VAL C 567 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N VAL C 567 " --> pdb=" O ARG C 557 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N HIS C 559 " --> pdb=" O ARG C 565 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ARG C 565 " --> pdb=" O HIS C 559 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 602 through 606 286 hydrogen bonds defined for protein. 702 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: 0.59 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 1888 1.34 - 1.47: 1123 1.47 - 1.60: 2078 1.60 - 1.74: 0 1.74 - 1.87: 45 Bond restraints: 5134 Sorted by residual: bond pdb=" C LYS C 303 " pdb=" N PRO C 304 " ideal model delta sigma weight residual 1.334 1.397 -0.063 2.34e-02 1.83e+03 7.19e+00 bond pdb=" C1 PAM B 401 " pdb=" O1 PAM B 401 " ideal model delta sigma weight residual 1.250 1.202 0.048 2.00e-02 2.50e+03 5.86e+00 bond pdb=" CB CYS B 321 " pdb=" SG CYS B 321 " ideal model delta sigma weight residual 1.808 1.873 -0.065 3.30e-02 9.18e+02 3.88e+00 bond pdb=" CB SER B 187 " pdb=" OG SER B 187 " ideal model delta sigma weight residual 1.417 1.451 -0.034 2.00e-02 2.50e+03 2.82e+00 bond pdb=" C1 PAM B 401 " pdb=" C2 PAM B 401 " ideal model delta sigma weight residual 1.538 1.504 0.034 2.00e-02 2.50e+03 2.81e+00 ... (remaining 5129 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 6606 1.70 - 3.40: 430 3.40 - 5.10: 84 5.10 - 6.80: 14 6.80 - 8.50: 4 Bond angle restraints: 7138 Sorted by residual: angle pdb=" C GLY B 114 " pdb=" N CYS B 115 " pdb=" CA CYS B 115 " ideal model delta sigma weight residual 121.54 129.52 -7.98 1.91e+00 2.74e-01 1.74e+01 angle pdb=" CA ARG C 141 " pdb=" C ARG C 141 " pdb=" N ALA C 142 " ideal model delta sigma weight residual 119.56 117.20 2.36 5.80e-01 2.97e+00 1.65e+01 angle pdb=" N VAL C 381 " pdb=" CA VAL C 381 " pdb=" C VAL C 381 " ideal model delta sigma weight residual 112.04 107.30 4.74 1.40e+00 5.10e-01 1.14e+01 angle pdb=" CA LYS C 303 " pdb=" C LYS C 303 " pdb=" N PRO C 304 " ideal model delta sigma weight residual 118.44 123.77 -5.33 1.59e+00 3.96e-01 1.12e+01 angle pdb=" N SER C 179 " pdb=" CA SER C 179 " pdb=" C SER C 179 " ideal model delta sigma weight residual 108.67 113.78 -5.11 1.55e+00 4.16e-01 1.09e+01 ... (remaining 7133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.04: 2980 12.04 - 24.08: 84 24.08 - 36.13: 23 36.13 - 48.17: 10 48.17 - 60.21: 10 Dihedral angle restraints: 3107 sinusoidal: 245 harmonic: 2862 Sorted by residual: dihedral pdb=" CB CYS B 313 " pdb=" SG CYS B 313 " pdb=" SG CYS B 328 " pdb=" CB CYS B 328 " ideal model delta sinusoidal sigma weight residual 93.00 37.41 55.59 1 1.00e+01 1.00e-02 4.17e+01 dihedral pdb=" CB CYS B 105 " pdb=" SG CYS B 105 " pdb=" SG CYS B 113 " pdb=" CB CYS B 113 " ideal model delta sinusoidal sigma weight residual -86.00 -138.59 52.59 1 1.00e+01 1.00e-02 3.77e+01 dihedral pdb=" CA CYS B 320 " pdb=" C CYS B 320 " pdb=" N CYS B 321 " pdb=" CA CYS B 321 " ideal model delta harmonic sigma weight residual 180.00 159.06 20.94 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 3104 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 567 0.036 - 0.072: 252 0.072 - 0.108: 73 0.108 - 0.144: 37 0.144 - 0.180: 2 Chirality restraints: 931 Sorted by residual: chirality pdb=" CA CYS B 321 " pdb=" N CYS B 321 " pdb=" C CYS B 321 " pdb=" CB CYS B 321 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.14e-01 chirality pdb=" CA ILE C 163 " pdb=" N ILE C 163 " pdb=" C ILE C 163 " pdb=" CB ILE C 163 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CA CYS B 115 " pdb=" N CYS B 115 " pdb=" C CYS B 115 " pdb=" CB CYS B 115 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 928 not shown) Planarity restraints: 1040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 145 " -0.014 2.00e-02 2.50e+03 2.73e-02 7.45e+00 pdb=" C LYS B 145 " 0.047 2.00e-02 2.50e+03 pdb=" O LYS B 145 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU B 146 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 72 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.34e+00 pdb=" C GLN B 72 " -0.040 2.00e-02 2.50e+03 pdb=" O GLN B 72 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU B 73 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 267 " 0.038 5.00e-02 4.00e+02 5.68e-02 5.16e+00 pdb=" N PRO C 268 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 268 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 268 " 0.031 5.00e-02 4.00e+02 ... (remaining 1037 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 582 2.74 - 3.28: 5035 3.28 - 3.82: 7526 3.82 - 4.36: 7462 4.36 - 4.90: 13462 Nonbonded interactions: 34067 Sorted by model distance: nonbonded pdb=" O MET A 122 " pdb=" N PHE A 127 " model vdw 2.201 3.120 nonbonded pdb=" O LYS B 292 " pdb=" N ASP B 297 " model vdw 2.208 3.120 nonbonded pdb=" O SER C 96 " pdb=" N SER C 114 " model vdw 2.268 3.120 nonbonded pdb=" O CYS B 320 " pdb=" N THR B 322 " model vdw 2.292 3.120 nonbonded pdb=" O TRP C 491 " pdb=" N ALA C 509 " model vdw 2.342 3.120 ... (remaining 34062 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.20 max=1.00 mean=0.95 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: 3.180 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.050 Find NCS groups from input model: 0.030 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3443 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 : 0.004 0.069 5156 Z= 0.230 Angle : 0.992 8.505 7180 Z= 0.587 Chirality : 0.047 0.180 931 Planarity : 0.006 0.057 1040 Dihedral : 7.618 54.388 1182 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 1.81 % Allowed : 9.66 % Favored : 88.53 % Rotamer: Outliers : 6.90 % Allowed : 8.05 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.23), residues: 994 helix: -1.41 (0.35), residues: 170 sheet: -1.53 (0.30), residues: 238 loop : -2.51 (0.22), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 48 PHE 0.000 0.000 PHE A 57 TRP 0.000 0.000 TRP A 73 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 5134) covalent geometry : angle 0.97807 ( 7138) SS BOND : bond 0.00410 ( 21) SS BOND : angle 2.40563 ( 42) hydrogen bonds : bond 0.24769 ( 286) hydrogen bonds : angle 8.62775 ( 702) Misc. bond : bond 0.04417 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 36 average time/residue: 0.0256 time to fit residues: 1.8920 Evaluate side-chains 28 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 328 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.0060 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 overall best weight: 2.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.211172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.195173 restraints weight = 18125.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.195173 restraints weight = 15700.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.196332 restraints weight = 14649.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.197323 restraints weight = 11622.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.197708 restraints weight = 10208.638| |-----------------------------------------------------------------------------| r_work (final): 0.4636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4636 r_free = 0.4636 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4616 r_free = 0.4616 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 140 | |-----------------------------------------------------------------------------| r_final: 0.4616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4122 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 5156 Z= 0.401 Angle : 1.070 10.039 7180 Z= 0.626 Chirality : 0.052 0.192 931 Planarity : 0.009 0.069 1040 Dihedral : 8.964 54.172 1016 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.50 % Allowed : 11.17 % Favored : 88.33 % Rotamer: Outliers : 2.30 % Allowed : 11.49 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.33 (0.22), residues: 994 helix: -1.32 (0.35), residues: 176 sheet: -1.28 (0.34), residues: 192 loop : -2.97 (0.20), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 48 PHE 0.000 0.000 PHE A 57 TRP 0.000 0.000 TRP A 73 Details of bonding type rmsd covalent geometry : bond 0.00661 ( 5134) covalent geometry : angle 1.04277 ( 7138) SS BOND : bond 0.01473 ( 21) SS BOND : angle 3.27765 ( 42) hydrogen bonds : bond 0.08128 ( 286) hydrogen bonds : angle 8.55776 ( 702) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.154 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.0212 time to fit residues: 1.1440 Evaluate side-chains 24 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain C residue 599 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 21 optimal weight: 30.0000 chunk 63 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 72 optimal weight: 0.1980 chunk 11 optimal weight: 3.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.207825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.190234 restraints weight = 18363.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.191947 restraints weight = 14641.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.193192 restraints weight = 11940.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.194247 restraints weight = 10048.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.195098 restraints weight = 8659.041| |-----------------------------------------------------------------------------| r_work (final): 0.4605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4605 r_free = 0.4605 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 140 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4601 r_free = 0.4601 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 168 | |-----------------------------------------------------------------------------| r_final: 0.4601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4203 moved from start: 0.5851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 5156 Z= 0.263 Angle : 0.820 7.503 7180 Z= 0.469 Chirality : 0.047 0.152 931 Planarity : 0.007 0.065 1040 Dihedral : 7.575 54.177 1014 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.40 % Allowed : 12.37 % Favored : 87.22 % Rotamer: Outliers : 4.60 % Allowed : 11.49 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.38 (0.24), residues: 994 helix: -0.59 (0.37), residues: 178 sheet: -1.76 (0.33), residues: 219 loop : -3.13 (0.21), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 48 PHE 0.000 0.000 PHE A 57 TRP 0.000 0.000 TRP A 73 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 5134) covalent geometry : angle 0.79911 ( 7138) SS BOND : bond 0.00885 ( 21) SS BOND : angle 2.51422 ( 42) hydrogen bonds : bond 0.06241 ( 286) hydrogen bonds : angle 7.44097 ( 702) Misc. bond : bond 0.00325 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: B 320 CYS cc_start: 0.0801 (OUTLIER) cc_final: 0.0453 (p) outliers start: 4 outliers final: 2 residues processed: 27 average time/residue: 0.0266 time to fit residues: 1.5290 Evaluate side-chains 26 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain C residue 599 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 21 optimal weight: 30.0000 chunk 48 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 78 optimal weight: 0.0970 chunk 55 optimal weight: 6.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.201924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.186669 restraints weight = 17947.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.187148 restraints weight = 15605.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.187921 restraints weight = 13298.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.188395 restraints weight = 11652.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.188690 restraints weight = 10364.090| |-----------------------------------------------------------------------------| r_work (final): 0.4532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4532 r_free = 0.4532 target_work(ls_wunit_k1) = 0.188 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 168 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4530 r_free = 0.4530 target_work(ls_wunit_k1) = 0.188 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 168 | |-----------------------------------------------------------------------------| r_final: 0.4530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4473 moved from start: 0.7811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 5156 Z= 0.369 Angle : 1.008 7.626 7180 Z= 0.595 Chirality : 0.050 0.165 931 Planarity : 0.008 0.075 1040 Dihedral : 9.099 59.860 1014 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.30 % Allowed : 18.11 % Favored : 81.59 % Rotamer: Outliers : 9.20 % Allowed : 10.34 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.91 (0.22), residues: 994 helix: -1.55 (0.35), residues: 168 sheet: -1.78 (0.35), residues: 179 loop : -3.36 (0.20), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 48 PHE 0.000 0.000 PHE A 57 TRP 0.000 0.000 TRP A 73 Details of bonding type rmsd covalent geometry : bond 0.00608 ( 5134) covalent geometry : angle 0.98827 ( 7138) SS BOND : bond 0.01063 ( 21) SS BOND : angle 2.79740 ( 42) hydrogen bonds : bond 0.08101 ( 286) hydrogen bonds : angle 8.90801 ( 702) Misc. bond : bond 0.00263 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 30 average time/residue: 0.0270 time to fit residues: 1.7227 Evaluate side-chains 27 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain C residue 304 PRO Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 599 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 90 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 40 optimal weight: 0.0770 chunk 34 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 83 optimal weight: 0.7980 chunk 66 optimal weight: 0.0040 chunk 50 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 overall best weight: 1.5752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.204340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.188439 restraints weight = 18210.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.189527 restraints weight = 16111.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.190675 restraints weight = 12894.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.191051 restraints weight = 11244.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.191281 restraints weight = 10028.229| |-----------------------------------------------------------------------------| r_work (final): 0.4566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4566 r_free = 0.4566 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 168 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4566 r_free = 0.4566 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 173 | |-----------------------------------------------------------------------------| r_final: 0.4566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4342 moved from start: 0.7854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5156 Z= 0.217 Angle : 0.806 10.967 7180 Z= 0.457 Chirality : 0.047 0.168 931 Planarity : 0.006 0.071 1040 Dihedral : 7.944 58.147 1014 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.20 % Allowed : 14.08 % Favored : 85.71 % Rotamer: Outliers : 5.75 % Allowed : 13.79 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.86 (0.23), residues: 994 helix: -1.35 (0.34), residues: 185 sheet: -1.96 (0.33), residues: 201 loop : -3.37 (0.21), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 48 PHE 0.000 0.000 PHE A 57 TRP 0.000 0.000 TRP A 73 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 5134) covalent geometry : angle 0.78221 ( 7138) SS BOND : bond 0.00700 ( 21) SS BOND : angle 2.64482 ( 42) hydrogen bonds : bond 0.05385 ( 286) hydrogen bonds : angle 7.74654 ( 702) Misc. bond : bond 0.00103 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 29 average time/residue: 0.0262 time to fit residues: 1.6251 Evaluate side-chains 28 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain C residue 304 PRO Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 599 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 70 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 98 optimal weight: 0.2980 chunk 94 optimal weight: 0.0870 chunk 39 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 53 optimal weight: 0.0970 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.208447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.193210 restraints weight = 18297.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.193666 restraints weight = 15937.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.195117 restraints weight = 13524.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.195771 restraints weight = 10460.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.196376 restraints weight = 8992.167| |-----------------------------------------------------------------------------| r_work (final): 0.4629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4629 r_free = 0.4629 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 173 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4629 r_free = 0.4629 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 173 | |-----------------------------------------------------------------------------| r_final: 0.4629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4122 moved from start: 0.7707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5156 Z= 0.122 Angle : 0.622 6.864 7180 Z= 0.344 Chirality : 0.045 0.135 931 Planarity : 0.005 0.056 1040 Dihedral : 6.291 57.977 1014 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.16 % Favored : 89.64 % Rotamer: Outliers : 3.45 % Allowed : 18.39 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.24), residues: 994 helix: -0.30 (0.37), residues: 187 sheet: -1.69 (0.34), residues: 214 loop : -3.25 (0.21), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 48 PHE 0.000 0.000 PHE A 57 TRP 0.000 0.000 TRP A 73 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 5134) covalent geometry : angle 0.61221 ( 7138) SS BOND : bond 0.00407 ( 21) SS BOND : angle 1.57900 ( 42) hydrogen bonds : bond 0.03372 ( 286) hydrogen bonds : angle 6.20355 ( 702) Misc. bond : bond 0.00065 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.165 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 26 average time/residue: 0.0240 time to fit residues: 1.3653 Evaluate side-chains 25 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain B residue 328 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 37 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 53 optimal weight: 0.2980 chunk 55 optimal weight: 0.0870 chunk 88 optimal weight: 2.9990 chunk 47 optimal weight: 0.0020 chunk 69 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.6168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.207795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.191073 restraints weight = 18227.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.192520 restraints weight = 14469.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.193681 restraints weight = 11893.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.194660 restraints weight = 9965.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.195198 restraints weight = 8555.994| |-----------------------------------------------------------------------------| r_work (final): 0.4615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4615 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4615 r_free = 0.4615 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 173 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4614 r_free = 0.4614 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 178 | |-----------------------------------------------------------------------------| r_final: 0.4614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4180 moved from start: 0.7879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5156 Z= 0.130 Angle : 0.601 6.781 7180 Z= 0.332 Chirality : 0.044 0.132 931 Planarity : 0.005 0.054 1040 Dihedral : 5.910 56.317 1014 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.27 % Favored : 87.63 % Rotamer: Outliers : 2.30 % Allowed : 20.69 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.25), residues: 994 helix: 0.18 (0.39), residues: 187 sheet: -1.66 (0.33), residues: 229 loop : -3.04 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 48 PHE 0.000 0.000 PHE A 57 TRP 0.000 0.000 TRP A 73 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 5134) covalent geometry : angle 0.58840 ( 7138) SS BOND : bond 0.00455 ( 21) SS BOND : angle 1.69159 ( 42) hydrogen bonds : bond 0.03474 ( 286) hydrogen bonds : angle 5.87298 ( 702) Misc. bond : bond 0.00053 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.119 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 26 average time/residue: 0.0266 time to fit residues: 1.4691 Evaluate side-chains 25 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain B residue 328 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 43 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.198353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.181213 restraints weight = 17700.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.182353 restraints weight = 16405.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.183011 restraints weight = 13629.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.183803 restraints weight = 11583.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.183973 restraints weight = 10967.057| |-----------------------------------------------------------------------------| r_work (final): 0.4485 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4485 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4485 r_free = 0.4485 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 178 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4485 r_free = 0.4485 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 193 | |-----------------------------------------------------------------------------| r_final: 0.4485 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4695 moved from start: 0.9836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 5156 Z= 0.487 Angle : 1.171 10.582 7180 Z= 0.690 Chirality : 0.053 0.189 931 Planarity : 0.008 0.066 1040 Dihedral : 10.013 55.873 1014 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.60 % Allowed : 20.93 % Favored : 78.47 % Rotamer: Outliers : 4.60 % Allowed : 18.39 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.32 (0.22), residues: 994 helix: -1.86 (0.34), residues: 167 sheet: -2.39 (0.36), residues: 173 loop : -3.52 (0.20), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 48 PHE 0.000 0.000 PHE A 57 TRP 0.000 0.000 TRP A 73 Details of bonding type rmsd covalent geometry : bond 0.00798 ( 5134) covalent geometry : angle 1.14122 ( 7138) SS BOND : bond 0.01192 ( 21) SS BOND : angle 3.60614 ( 42) hydrogen bonds : bond 0.09675 ( 286) hydrogen bonds : angle 10.00682 ( 702) Misc. bond : bond 0.00117 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.187 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 27 average time/residue: 0.0258 time to fit residues: 1.5325 Evaluate side-chains 25 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 CYS Chi-restraints excluded: chain B residue 328 CYS Chi-restraints excluded: chain C residue 310 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.4980 chunk 56 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 20 optimal weight: 0.0980 chunk 93 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 40 optimal weight: 0.3980 chunk 61 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.204834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.189515 restraints weight = 17961.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.190035 restraints weight = 15291.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.190690 restraints weight = 13660.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.191590 restraints weight = 11366.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.191685 restraints weight = 10296.814| |-----------------------------------------------------------------------------| r_work (final): 0.4578 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4578 r_free = 0.4578 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 193 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4578 r_free = 0.4578 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 188 | |-----------------------------------------------------------------------------| r_final: 0.4578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4279 moved from start: 0.9346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 5156 Z= 0.148 Angle : 0.676 7.586 7180 Z= 0.380 Chirality : 0.045 0.138 931 Planarity : 0.006 0.067 1040 Dihedral : 7.109 56.455 1014 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.67 % Favored : 88.23 % Rotamer: Outliers : 2.30 % Allowed : 19.54 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.90 (0.23), residues: 994 helix: -1.21 (0.34), residues: 199 sheet: -2.15 (0.34), residues: 193 loop : -3.42 (0.21), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 48 PHE 0.000 0.000 PHE A 57 TRP 0.000 0.000 TRP A 73 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 5134) covalent geometry : angle 0.66179 ( 7138) SS BOND : bond 0.00341 ( 21) SS BOND : angle 1.91220 ( 42) hydrogen bonds : bond 0.03891 ( 286) hydrogen bonds : angle 7.16737 ( 702) Misc. bond : bond 0.00092 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.181 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 25 average time/residue: 0.0251 time to fit residues: 1.3935 Evaluate side-chains 24 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 328 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 42 optimal weight: 4.9990 chunk 72 optimal weight: 0.0070 chunk 33 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 0.0170 chunk 58 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 overall best weight: 2.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.201110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.185506 restraints weight = 17872.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.185805 restraints weight = 14830.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.187268 restraints weight = 13344.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.187863 restraints weight = 10153.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.188133 restraints weight = 9438.705| |-----------------------------------------------------------------------------| r_work (final): 0.4538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4539 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4539 r_free = 0.4539 target_work(ls_wunit_k1) = 0.188 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 188 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4538 r_free = 0.4538 target_work(ls_wunit_k1) = 0.188 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 193 | |-----------------------------------------------------------------------------| r_final: 0.4538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4477 moved from start: 0.9828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5156 Z= 0.259 Angle : 0.797 7.968 7180 Z= 0.457 Chirality : 0.046 0.138 931 Planarity : 0.006 0.068 1040 Dihedral : 7.827 54.278 1014 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 18.91 % Favored : 80.99 % Rotamer: Outliers : 1.15 % Allowed : 19.54 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.00 (0.23), residues: 994 helix: -1.26 (0.35), residues: 187 sheet: -2.20 (0.35), residues: 186 loop : -3.47 (0.21), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 48 PHE 0.000 0.000 PHE A 57 TRP 0.000 0.000 TRP A 73 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 5134) covalent geometry : angle 0.77171 ( 7138) SS BOND : bond 0.00684 ( 21) SS BOND : angle 2.73089 ( 42) hydrogen bonds : bond 0.05916 ( 286) hydrogen bonds : angle 7.97832 ( 702) Misc. bond : bond 0.00043 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.108 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 25 average time/residue: 0.0211 time to fit residues: 1.1509 Evaluate side-chains 25 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 328 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 90 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.200118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.184237 restraints weight = 18048.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.185151 restraints weight = 16818.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.186691 restraints weight = 13270.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.187095 restraints weight = 10533.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.187576 restraints weight = 9573.850| |-----------------------------------------------------------------------------| r_work (final): 0.4537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4537 r_free = 0.4537 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 193 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4537 r_free = 0.4537 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 193 | |-----------------------------------------------------------------------------| r_final: 0.4537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4520 moved from start: 1.0494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 5156 Z= 0.262 Angle : 0.810 8.372 7180 Z= 0.465 Chirality : 0.046 0.140 931 Planarity : 0.007 0.073 1040 Dihedral : 8.068 54.779 1014 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 17.30 % Favored : 82.60 % Rotamer: Outliers : 1.15 % Allowed : 18.39 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.19 (0.23), residues: 994 helix: -1.47 (0.34), residues: 189 sheet: -2.48 (0.35), residues: 181 loop : -3.51 (0.21), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 48 PHE 0.000 0.000 PHE A 57 TRP 0.000 0.000 TRP A 73 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 5134) covalent geometry : angle 0.78822 ( 7138) SS BOND : bond 0.00606 ( 21) SS BOND : angle 2.54934 ( 42) hydrogen bonds : bond 0.06024 ( 286) hydrogen bonds : angle 8.26868 ( 702) Misc. bond : bond 0.00103 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1020.73 seconds wall clock time: 18 minutes 4.20 seconds (1084.20 seconds total)