Starting phenix.real_space_refine on Mon Jul 28 14:38:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kak_22773/07_2025/7kak_22773.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kak_22773/07_2025/7kak_22773.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kak_22773/07_2025/7kak_22773.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kak_22773/07_2025/7kak_22773.map" model { file = "/net/cci-nas-00/data/ceres_data/7kak_22773/07_2025/7kak_22773.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kak_22773/07_2025/7kak_22773.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.004 sd= 0.055 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 49 5.16 5 C 6796 2.51 5 N 1789 2.21 5 O 1803 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10437 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3331 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain breaks: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 8, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 74 Chain: "C" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 440 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 54} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 245 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 30} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 3612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3612 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 31, 'TRANS': 438} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 78 Chain: "E" Number of atoms: 1355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1355 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 58 Chain: "F" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1454 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 15, 'TRANS': 178} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Time building chain proxies: 6.32, per 1000 atoms: 0.61 Number of scatterers: 10437 At special positions: 0 Unit cell: (107.16, 125.4, 136.8, 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 49 16.00 O 1803 8.00 N 1789 7.00 C 6796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.2 seconds 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2562 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 7 sheets defined 67.8% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 28 through 48 Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 82 through 99 removed outlier: 3.506A pdb=" N ILE A 86 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 94 " --> pdb=" O MET A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 136 removed outlier: 3.985A pdb=" N LEU A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 removed outlier: 4.142A pdb=" N GLY A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 174 removed outlier: 4.101A pdb=" N GLY A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 196 removed outlier: 4.271A pdb=" N LEU A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN A 188 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 196 " --> pdb=" O SER A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 227 through 236 Processing helix chain 'A' and resid 243 through 262 removed outlier: 3.570A pdb=" N LEU A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY A 262 " --> pdb=" O ILE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 314 removed outlier: 3.511A pdb=" N GLN A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG A 313 " --> pdb=" O MET A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 324 Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 350 through 357 Processing helix chain 'A' and resid 357 through 383 removed outlier: 4.271A pdb=" N GLU A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A 382 " --> pdb=" O THR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 398 removed outlier: 3.942A pdb=" N LYS A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 439 removed outlier: 3.890A pdb=" N GLU A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) Proline residue: A 418 - end of helix removed outlier: 3.979A pdb=" N ALA A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 439 " --> pdb=" O SER A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 463 removed outlier: 3.589A pdb=" N ILE A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 26 Processing helix chain 'C' and resid 30 through 68 removed outlier: 3.677A pdb=" N PHE C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Proline residue: C 61 - end of helix removed outlier: 3.611A pdb=" N ALA C 68 " --> pdb=" O ASN C 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 123 removed outlier: 3.842A pdb=" N VAL B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B 100 " --> pdb=" O PRO B 96 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 33 Proline residue: D 29 - end of helix Processing helix chain 'D' and resid 56 through 68 removed outlier: 4.151A pdb=" N LEU D 68 " --> pdb=" O LYS D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 97 removed outlier: 4.204A pdb=" N ILE D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ALA D 79 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 197 removed outlier: 3.753A pdb=" N ILE D 196 " --> pdb=" O PRO D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 228 removed outlier: 4.578A pdb=" N LEU D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) Proline residue: D 218 - end of helix Processing helix chain 'D' and resid 237 through 247 removed outlier: 3.700A pdb=" N ARG D 246 " --> pdb=" O GLY D 242 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 262 removed outlier: 4.032A pdb=" N VAL D 258 " --> pdb=" O GLY D 254 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN D 259 " --> pdb=" O GLY D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 271 removed outlier: 3.881A pdb=" N GLU D 269 " --> pdb=" O GLU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 291 removed outlier: 3.675A pdb=" N ASP D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 removed outlier: 3.826A pdb=" N ILE D 306 " --> pdb=" O VAL D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 323 Processing helix chain 'D' and resid 332 through 357 removed outlier: 4.067A pdb=" N GLU D 338 " --> pdb=" O GLU D 334 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER D 341 " --> pdb=" O TYR D 337 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER D 345 " --> pdb=" O SER D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 375 removed outlier: 3.664A pdb=" N GLN D 375 " --> pdb=" O GLN D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 387 removed outlier: 3.572A pdb=" N LEU D 385 " --> pdb=" O SER D 382 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN D 386 " --> pdb=" O PRO D 383 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU D 387 " --> pdb=" O LEU D 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 382 through 387' Processing helix chain 'D' and resid 391 through 399 Processing helix chain 'D' and resid 408 through 414 Processing helix chain 'D' and resid 418 through 423 Processing helix chain 'D' and resid 431 through 443 removed outlier: 3.818A pdb=" N SER D 437 " --> pdb=" O ASP D 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 36 Proline residue: E 9 - end of helix Processing helix chain 'E' and resid 46 through 60 Processing helix chain 'E' and resid 71 through 104 removed outlier: 4.315A pdb=" N GLN E 97 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN E 104 " --> pdb=" O ALA E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 138 removed outlier: 3.652A pdb=" N GLN E 114 " --> pdb=" O ASP E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 167 removed outlier: 3.934A pdb=" N PHE E 146 " --> pdb=" O GLY E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 180 Processing helix chain 'F' and resid 31 through 56 removed outlier: 4.108A pdb=" N ASP F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 87 removed outlier: 4.604A pdb=" N SER F 72 " --> pdb=" O ASN F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 107 Processing helix chain 'F' and resid 113 through 135 removed outlier: 4.108A pdb=" N ALA F 117 " --> pdb=" O PRO F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 152 Processing helix chain 'F' and resid 157 through 171 Processing helix chain 'F' and resid 172 through 187 Processing helix chain 'F' and resid 192 through 203 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 removed outlier: 6.618A pdb=" N GLU A 19 " --> pdb=" O VAL B 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 211 removed outlier: 3.768A pdb=" N GLU A 210 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASN D 7 " --> pdb=" O ILE D 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 280 through 281 removed outlier: 3.548A pdb=" N TYR A 281 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 267 " --> pdb=" O TYR A 281 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.613A pdb=" N VAL A 325 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 448 through 457 removed outlier: 5.975A pdb=" N ILE D 450 " --> pdb=" O ARG D 476 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG D 476 " --> pdb=" O ILE D 450 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS D 452 " --> pdb=" O LYS D 474 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE D 454 " --> pdb=" O VAL D 472 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 558 through 565 removed outlier: 5.942A pdb=" N LEU D 550 " --> pdb=" O PRO D 561 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE D 548 " --> pdb=" O PHE D 563 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE D 549 " --> pdb=" O HIS D 604 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN D 617 " --> pdb=" O LEU D 603 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 13 through 15 677 hydrogen bonds defined for protein. 2016 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: 3.42 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3307 1.34 - 1.46: 2203 1.46 - 1.58: 5075 1.58 - 1.69: 0 1.69 - 1.81: 85 Bond restraints: 10670 Sorted by residual: bond pdb=" C PRO F 57 " pdb=" N PRO F 58 " ideal model delta sigma weight residual 1.330 1.357 -0.027 1.25e-02 6.40e+03 4.57e+00 bond pdb=" N PRO D 29 " pdb=" CA PRO D 29 " ideal model delta sigma weight residual 1.471 1.458 0.013 1.29e-02 6.01e+03 9.96e-01 bond pdb=" CB PRO D 536 " pdb=" CG PRO D 536 " ideal model delta sigma weight residual 1.492 1.538 -0.046 5.00e-02 4.00e+02 8.43e-01 bond pdb=" CA ILE D 361 " pdb=" CB ILE D 361 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 7.15e-01 bond pdb=" C LEU D 28 " pdb=" O LEU D 28 " ideal model delta sigma weight residual 1.244 1.236 0.008 1.00e-02 1.00e+04 5.80e-01 ... (remaining 10665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 14307 1.79 - 3.58: 160 3.58 - 5.37: 29 5.37 - 7.16: 8 7.16 - 8.95: 2 Bond angle restraints: 14506 Sorted by residual: angle pdb=" N PRO D 29 " pdb=" CA PRO D 29 " pdb=" CB PRO D 29 " ideal model delta sigma weight residual 103.44 110.15 -6.71 1.12e+00 7.97e-01 3.59e+01 angle pdb=" CA LEU D 28 " pdb=" C LEU D 28 " pdb=" N PRO D 29 " ideal model delta sigma weight residual 120.77 116.97 3.80 9.70e-01 1.06e+00 1.54e+01 angle pdb=" N SER A 289 " pdb=" CA SER A 289 " pdb=" C SER A 289 " ideal model delta sigma weight residual 111.02 114.52 -3.50 1.22e+00 6.72e-01 8.24e+00 angle pdb=" C ILE A 417 " pdb=" CA ILE A 417 " pdb=" CB ILE A 417 " ideal model delta sigma weight residual 114.00 110.53 3.47 1.31e+00 5.83e-01 7.01e+00 angle pdb=" CA LEU A 63 " pdb=" CB LEU A 63 " pdb=" CG LEU A 63 " ideal model delta sigma weight residual 116.30 125.25 -8.95 3.50e+00 8.16e-02 6.54e+00 ... (remaining 14501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 5940 17.85 - 35.70: 382 35.70 - 53.56: 50 53.56 - 71.41: 5 71.41 - 89.26: 4 Dihedral angle restraints: 6381 sinusoidal: 2413 harmonic: 3968 Sorted by residual: dihedral pdb=" CB GLU A 169 " pdb=" CG GLU A 169 " pdb=" CD GLU A 169 " pdb=" OE1 GLU A 169 " ideal model delta sinusoidal sigma weight residual 0.00 89.26 -89.26 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" N PRO D 29 " pdb=" C PRO D 29 " pdb=" CA PRO D 29 " pdb=" CB PRO D 29 " ideal model delta harmonic sigma weight residual 115.10 122.79 -7.69 0 2.50e+00 1.60e-01 9.47e+00 dihedral pdb=" CA ARG E 48 " pdb=" CB ARG E 48 " pdb=" CG ARG E 48 " pdb=" CD ARG E 48 " ideal model delta sinusoidal sigma weight residual -60.00 -110.93 50.93 3 1.50e+01 4.44e-03 8.96e+00 ... (remaining 6378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1379 0.046 - 0.092: 270 0.092 - 0.138: 40 0.138 - 0.184: 0 0.184 - 0.230: 2 Chirality restraints: 1691 Sorted by residual: chirality pdb=" CA PRO D 29 " pdb=" N PRO D 29 " pdb=" C PRO D 29 " pdb=" CB PRO D 29 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB ILE D 473 " pdb=" CA ILE D 473 " pdb=" CG1 ILE D 473 " pdb=" CG2 ILE D 473 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" CA THR A 83 " pdb=" N THR A 83 " pdb=" C THR A 83 " pdb=" CB THR A 83 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.09e-01 ... (remaining 1688 not shown) Planarity restraints: 1816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 141 " 0.020 2.00e-02 2.50e+03 1.30e-02 4.24e+00 pdb=" CG TRP E 141 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP E 141 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP E 141 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 141 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 141 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 141 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 141 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 141 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 141 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 426 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO D 427 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 427 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 427 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 56 " -0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO F 57 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO F 57 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 57 " -0.025 5.00e-02 4.00e+02 ... (remaining 1813 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2176 2.78 - 3.31: 10222 3.31 - 3.84: 16711 3.84 - 4.37: 16831 4.37 - 4.90: 30500 Nonbonded interactions: 76440 Sorted by model distance: nonbonded pdb=" O PHE A 198 " pdb=" OH TYR C 53 " model vdw 2.246 3.040 nonbonded pdb=" OE1 GLU A 79 " pdb=" OH TYR A 139 " model vdw 2.287 3.040 nonbonded pdb=" OD1 ASN E 155 " pdb=" NH2 ARG E 159 " model vdw 2.291 3.120 nonbonded pdb=" NH1 ARG E 159 " pdb=" O ALA F 106 " model vdw 2.293 3.120 nonbonded pdb=" O SER D 228 " pdb=" OG SER D 228 " model vdw 2.296 3.040 ... (remaining 76435 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 26.570 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 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 : 0.003 0.046 10670 Z= 0.121 Angle : 0.543 8.951 14506 Z= 0.291 Chirality : 0.037 0.230 1691 Planarity : 0.004 0.047 1816 Dihedral : 11.574 89.261 3819 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.22), residues: 1341 helix: -0.01 (0.17), residues: 871 sheet: -2.04 (0.60), residues: 63 loop : -2.52 (0.27), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP E 141 HIS 0.004 0.001 HIS C 59 PHE 0.011 0.001 PHE E 42 TYR 0.006 0.001 TYR E 51 ARG 0.002 0.000 ARG D 540 Details of bonding type rmsd hydrogen bonds : bond 0.11197 ( 677) hydrogen bonds : angle 4.62827 ( 2016) covalent geometry : bond 0.00252 (10670) covalent geometry : angle 0.54291 (14506) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8840 (tmm) cc_final: 0.7619 (mmp) REVERT: A 125 LEU cc_start: 0.9782 (tt) cc_final: 0.9554 (pp) REVERT: A 131 CYS cc_start: 0.9122 (m) cc_final: 0.8727 (m) REVERT: D 217 LEU cc_start: 0.9299 (tp) cc_final: 0.9096 (tt) REVERT: E 121 LYS cc_start: 0.9305 (mmtm) cc_final: 0.9104 (pttt) REVERT: E 162 MET cc_start: 0.9115 (tpp) cc_final: 0.8902 (tpp) REVERT: F 177 ARG cc_start: 0.9150 (mtp-110) cc_final: 0.8686 (mmp-170) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.2965 time to fit residues: 60.5656 Evaluate side-chains 98 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 54 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 156 GLN A 261 GLN D 61 GLN D 444 GLN D 604 HIS E 95 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.053162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.042539 restraints weight = 73237.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.043617 restraints weight = 39704.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.044321 restraints weight = 26662.974| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10670 Z= 0.145 Angle : 0.607 10.489 14506 Z= 0.290 Chirality : 0.037 0.121 1691 Planarity : 0.004 0.054 1816 Dihedral : 3.252 14.920 1474 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.23 % Allowed : 11.53 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.23), residues: 1341 helix: 1.08 (0.18), residues: 881 sheet: -1.88 (0.62), residues: 73 loop : -1.97 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 141 HIS 0.004 0.001 HIS D 56 PHE 0.015 0.001 PHE E 42 TYR 0.015 0.001 TYR F 100 ARG 0.004 0.000 ARG E 80 Details of bonding type rmsd hydrogen bonds : bond 0.03685 ( 677) hydrogen bonds : angle 3.83206 ( 2016) covalent geometry : bond 0.00324 (10670) covalent geometry : angle 0.60725 (14506) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8905 (tmm) cc_final: 0.7399 (mmp) REVERT: A 69 MET cc_start: 0.9400 (tpp) cc_final: 0.9180 (tpp) REVERT: A 131 CYS cc_start: 0.9392 (m) cc_final: 0.8906 (m) REVERT: D 583 MET cc_start: 0.9010 (tpp) cc_final: 0.8691 (tpp) REVERT: E 162 MET cc_start: 0.9330 (tpp) cc_final: 0.9081 (tpp) outliers start: 13 outliers final: 10 residues processed: 112 average time/residue: 0.2168 time to fit residues: 35.2814 Evaluate side-chains 100 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 40 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.053193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.042575 restraints weight = 73836.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.043648 restraints weight = 39876.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.044367 restraints weight = 26722.717| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10670 Z= 0.129 Angle : 0.581 10.728 14506 Z= 0.277 Chirality : 0.037 0.199 1691 Planarity : 0.004 0.049 1816 Dihedral : 3.264 16.028 1474 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.42 % Allowed : 15.22 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.24), residues: 1341 helix: 1.48 (0.18), residues: 881 sheet: -1.53 (0.65), residues: 73 loop : -1.70 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 141 HIS 0.003 0.001 HIS F 132 PHE 0.020 0.001 PHE D 563 TYR 0.009 0.001 TYR A 457 ARG 0.011 0.000 ARG F 88 Details of bonding type rmsd hydrogen bonds : bond 0.03524 ( 677) hydrogen bonds : angle 3.69885 ( 2016) covalent geometry : bond 0.00290 (10670) covalent geometry : angle 0.58123 (14506) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8942 (tmm) cc_final: 0.7472 (mmp) REVERT: A 69 MET cc_start: 0.9419 (tpp) cc_final: 0.9092 (tpp) REVERT: A 131 CYS cc_start: 0.9368 (m) cc_final: 0.8862 (m) REVERT: A 368 MET cc_start: 0.8972 (tpt) cc_final: 0.8708 (tpt) REVERT: A 401 MET cc_start: 0.7695 (pmm) cc_final: 0.7478 (pmm) REVERT: D 583 MET cc_start: 0.9024 (tpp) cc_final: 0.8708 (tpp) REVERT: E 125 ASP cc_start: 0.8571 (m-30) cc_final: 0.8334 (p0) REVERT: E 162 MET cc_start: 0.9314 (tpp) cc_final: 0.9035 (tpp) REVERT: F 137 MET cc_start: 0.7518 (mpp) cc_final: 0.7242 (mpp) outliers start: 15 outliers final: 12 residues processed: 106 average time/residue: 0.2092 time to fit residues: 32.9754 Evaluate side-chains 102 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 17 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 29 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 overall best weight: 3.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 529 GLN ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.051667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.041071 restraints weight = 73789.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.042080 restraints weight = 40207.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.042744 restraints weight = 27301.201| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10670 Z= 0.210 Angle : 0.634 10.416 14506 Z= 0.308 Chirality : 0.038 0.195 1691 Planarity : 0.004 0.047 1816 Dihedral : 3.471 15.289 1474 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.17 % Allowed : 17.11 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.24), residues: 1341 helix: 1.73 (0.18), residues: 881 sheet: -1.27 (0.65), residues: 73 loop : -1.57 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 141 HIS 0.006 0.001 HIS D 534 PHE 0.019 0.002 PHE E 42 TYR 0.016 0.001 TYR C 53 ARG 0.007 0.000 ARG F 50 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 677) hydrogen bonds : angle 3.82680 ( 2016) covalent geometry : bond 0.00465 (10670) covalent geometry : angle 0.63439 (14506) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8999 (tmm) cc_final: 0.7515 (mmp) REVERT: A 131 CYS cc_start: 0.9374 (m) cc_final: 0.8868 (m) REVERT: A 166 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9337 (tt) REVERT: D 252 MET cc_start: 0.9191 (ppp) cc_final: 0.8896 (ppp) REVERT: E 162 MET cc_start: 0.9334 (tpp) cc_final: 0.9099 (tpp) REVERT: F 137 MET cc_start: 0.7619 (mpp) cc_final: 0.7365 (mpp) outliers start: 23 outliers final: 11 residues processed: 105 average time/residue: 0.1969 time to fit residues: 31.2881 Evaluate side-chains 96 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 115 optimal weight: 7.9990 chunk 123 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.051432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.040753 restraints weight = 74938.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.041761 restraints weight = 40860.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.042431 restraints weight = 27823.191| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10670 Z= 0.204 Angle : 0.622 10.668 14506 Z= 0.302 Chirality : 0.038 0.195 1691 Planarity : 0.004 0.047 1816 Dihedral : 3.524 16.920 1474 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.65 % Allowed : 17.96 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.24), residues: 1341 helix: 1.85 (0.18), residues: 876 sheet: -1.11 (0.66), residues: 73 loop : -1.44 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 141 HIS 0.005 0.001 HIS D 534 PHE 0.016 0.001 PHE E 42 TYR 0.018 0.001 TYR F 100 ARG 0.005 0.000 ARG F 50 Details of bonding type rmsd hydrogen bonds : bond 0.03849 ( 677) hydrogen bonds : angle 3.85427 ( 2016) covalent geometry : bond 0.00452 (10670) covalent geometry : angle 0.62231 (14506) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9007 (tmm) cc_final: 0.7511 (mmp) REVERT: A 69 MET cc_start: 0.9451 (tpp) cc_final: 0.9209 (tpp) REVERT: A 78 MET cc_start: 0.8681 (mmm) cc_final: 0.7931 (tpp) REVERT: A 131 CYS cc_start: 0.9385 (m) cc_final: 0.8900 (m) REVERT: A 166 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.9316 (tt) REVERT: A 368 MET cc_start: 0.9125 (tpt) cc_final: 0.8800 (tpt) REVERT: D 252 MET cc_start: 0.9172 (ppp) cc_final: 0.8845 (ppp) REVERT: E 121 LYS cc_start: 0.9143 (mtmm) cc_final: 0.8849 (pttm) REVERT: E 162 MET cc_start: 0.9267 (tpp) cc_final: 0.8803 (tpp) outliers start: 28 outliers final: 18 residues processed: 109 average time/residue: 0.2051 time to fit residues: 33.3281 Evaluate side-chains 101 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 106 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 6 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 114 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.3223 r_free = 0.3223 target = 0.052009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.041408 restraints weight = 74779.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.042451 restraints weight = 40150.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.043152 restraints weight = 26914.213| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10670 Z= 0.127 Angle : 0.603 13.669 14506 Z= 0.284 Chirality : 0.037 0.205 1691 Planarity : 0.004 0.048 1816 Dihedral : 3.422 16.483 1474 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.08 % Allowed : 20.13 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.24), residues: 1341 helix: 2.02 (0.18), residues: 875 sheet: -0.96 (0.66), residues: 75 loop : -1.28 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 176 HIS 0.004 0.001 HIS F 132 PHE 0.012 0.001 PHE D 15 TYR 0.007 0.001 TYR E 158 ARG 0.004 0.000 ARG F 50 Details of bonding type rmsd hydrogen bonds : bond 0.03591 ( 677) hydrogen bonds : angle 3.59864 ( 2016) covalent geometry : bond 0.00285 (10670) covalent geometry : angle 0.60263 (14506) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8988 (tmm) cc_final: 0.7507 (mmp) REVERT: A 69 MET cc_start: 0.9452 (tpp) cc_final: 0.9206 (tpp) REVERT: A 78 MET cc_start: 0.8499 (mmm) cc_final: 0.7965 (tpp) REVERT: A 131 CYS cc_start: 0.9375 (m) cc_final: 0.8884 (m) REVERT: A 166 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9336 (tt) REVERT: A 368 MET cc_start: 0.9063 (tpt) cc_final: 0.8736 (tpt) REVERT: D 252 MET cc_start: 0.9143 (ppp) cc_final: 0.8052 (ppp) REVERT: D 588 MET cc_start: 0.8390 (mmm) cc_final: 0.8070 (tpt) REVERT: E 23 PHE cc_start: 0.9191 (t80) cc_final: 0.8933 (t80) REVERT: E 125 ASP cc_start: 0.8695 (m-30) cc_final: 0.8448 (p0) REVERT: E 162 MET cc_start: 0.9232 (tpp) cc_final: 0.8847 (tpp) outliers start: 22 outliers final: 15 residues processed: 108 average time/residue: 0.2053 time to fit residues: 33.2072 Evaluate side-chains 101 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 45 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 95 optimal weight: 0.5980 chunk 125 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 HIS ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.050747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.040211 restraints weight = 75877.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.041215 restraints weight = 41295.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.041868 restraints weight = 28022.953| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10670 Z= 0.238 Angle : 0.678 11.866 14506 Z= 0.328 Chirality : 0.039 0.198 1691 Planarity : 0.004 0.046 1816 Dihedral : 3.663 19.678 1474 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.46 % Allowed : 21.27 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.24), residues: 1341 helix: 1.95 (0.18), residues: 877 sheet: -1.05 (0.66), residues: 75 loop : -1.25 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 141 HIS 0.005 0.001 HIS C 59 PHE 0.018 0.002 PHE E 42 TYR 0.024 0.001 TYR F 100 ARG 0.004 0.000 ARG F 128 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 677) hydrogen bonds : angle 3.88800 ( 2016) covalent geometry : bond 0.00526 (10670) covalent geometry : angle 0.67770 (14506) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9015 (tmm) cc_final: 0.7535 (mmp) REVERT: A 69 MET cc_start: 0.9487 (tpp) cc_final: 0.9251 (tpp) REVERT: A 78 MET cc_start: 0.8674 (mmm) cc_final: 0.7996 (tpp) REVERT: A 131 CYS cc_start: 0.9401 (m) cc_final: 0.8940 (m) REVERT: A 166 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9336 (tt) REVERT: D 252 MET cc_start: 0.9133 (ppp) cc_final: 0.8042 (ppp) REVERT: E 23 PHE cc_start: 0.9297 (t80) cc_final: 0.9039 (t80) REVERT: E 121 LYS cc_start: 0.9006 (pttp) cc_final: 0.8670 (pttm) REVERT: E 162 MET cc_start: 0.9264 (tpp) cc_final: 0.8888 (tpp) outliers start: 26 outliers final: 18 residues processed: 102 average time/residue: 0.2045 time to fit residues: 31.1092 Evaluate side-chains 100 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 54 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 375 GLN ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.050535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.040040 restraints weight = 74894.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.041053 restraints weight = 40830.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.041705 restraints weight = 27603.344| |-----------------------------------------------------------------------------| r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10670 Z= 0.191 Angle : 0.657 11.907 14506 Z= 0.312 Chirality : 0.038 0.211 1691 Planarity : 0.004 0.048 1816 Dihedral : 3.656 17.823 1474 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.08 % Allowed : 21.83 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.24), residues: 1341 helix: 1.96 (0.18), residues: 880 sheet: -1.03 (0.65), residues: 75 loop : -1.21 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 176 HIS 0.005 0.001 HIS D 534 PHE 0.015 0.001 PHE E 42 TYR 0.017 0.001 TYR C 53 ARG 0.004 0.000 ARG F 128 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 677) hydrogen bonds : angle 3.81080 ( 2016) covalent geometry : bond 0.00428 (10670) covalent geometry : angle 0.65651 (14506) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9017 (tmm) cc_final: 0.7490 (mmp) REVERT: A 69 MET cc_start: 0.9466 (tpp) cc_final: 0.9172 (tpp) REVERT: A 78 MET cc_start: 0.8689 (mmm) cc_final: 0.8107 (tpp) REVERT: A 131 CYS cc_start: 0.9395 (m) cc_final: 0.8937 (m) REVERT: A 166 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9335 (tt) REVERT: A 368 MET cc_start: 0.9067 (tpt) cc_final: 0.8099 (mmm) REVERT: D 252 MET cc_start: 0.9065 (ppp) cc_final: 0.7745 (ppp) REVERT: E 23 PHE cc_start: 0.9280 (t80) cc_final: 0.9015 (t80) REVERT: E 121 LYS cc_start: 0.9129 (pttp) cc_final: 0.8834 (pttm) REVERT: E 162 MET cc_start: 0.9248 (tpp) cc_final: 0.8896 (tpp) REVERT: F 137 MET cc_start: 0.7853 (mpp) cc_final: 0.7520 (pmm) outliers start: 22 outliers final: 16 residues processed: 103 average time/residue: 0.1968 time to fit residues: 30.1215 Evaluate side-chains 101 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 8 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.050531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.040057 restraints weight = 75903.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.041076 restraints weight = 41327.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.041741 restraints weight = 27853.049| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10670 Z= 0.179 Angle : 0.664 11.689 14506 Z= 0.315 Chirality : 0.038 0.208 1691 Planarity : 0.004 0.047 1816 Dihedral : 3.646 21.399 1474 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.98 % Allowed : 21.74 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.24), residues: 1341 helix: 2.02 (0.18), residues: 879 sheet: -1.02 (0.65), residues: 75 loop : -1.16 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 141 HIS 0.005 0.001 HIS D 534 PHE 0.017 0.001 PHE B 106 TYR 0.016 0.001 TYR C 53 ARG 0.003 0.000 ARG F 128 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 677) hydrogen bonds : angle 3.77978 ( 2016) covalent geometry : bond 0.00404 (10670) covalent geometry : angle 0.66415 (14506) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9019 (tmm) cc_final: 0.7483 (mmp) REVERT: A 69 MET cc_start: 0.9470 (tpp) cc_final: 0.9222 (tpp) REVERT: A 78 MET cc_start: 0.8660 (mmm) cc_final: 0.8111 (tpp) REVERT: A 131 CYS cc_start: 0.9400 (m) cc_final: 0.8944 (m) REVERT: A 166 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9338 (tt) REVERT: A 401 MET cc_start: 0.7684 (pmm) cc_final: 0.6972 (ptp) REVERT: D 252 MET cc_start: 0.9068 (ppp) cc_final: 0.7731 (ppp) REVERT: E 23 PHE cc_start: 0.9280 (t80) cc_final: 0.9016 (t80) REVERT: E 121 LYS cc_start: 0.9197 (pttp) cc_final: 0.8915 (pttm) outliers start: 21 outliers final: 16 residues processed: 101 average time/residue: 0.2031 time to fit residues: 30.5975 Evaluate side-chains 99 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 86 optimal weight: 0.0570 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.050861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.040449 restraints weight = 74786.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.041470 restraints weight = 40773.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.042135 restraints weight = 27458.302| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10670 Z= 0.150 Angle : 0.651 11.744 14506 Z= 0.306 Chirality : 0.038 0.207 1691 Planarity : 0.004 0.048 1816 Dihedral : 3.592 20.747 1474 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.51 % Allowed : 22.40 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.24), residues: 1341 helix: 2.06 (0.18), residues: 877 sheet: -1.16 (0.60), residues: 85 loop : -1.01 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 141 HIS 0.004 0.001 HIS D 534 PHE 0.012 0.001 PHE E 42 TYR 0.015 0.001 TYR C 53 ARG 0.005 0.000 ARG E 161 Details of bonding type rmsd hydrogen bonds : bond 0.03744 ( 677) hydrogen bonds : angle 3.68659 ( 2016) covalent geometry : bond 0.00339 (10670) covalent geometry : angle 0.65109 (14506) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9000 (tmm) cc_final: 0.7415 (mmp) REVERT: A 69 MET cc_start: 0.9473 (tpp) cc_final: 0.9224 (tpp) REVERT: A 78 MET cc_start: 0.8683 (mmm) cc_final: 0.8156 (tpp) REVERT: A 131 CYS cc_start: 0.9408 (m) cc_final: 0.8947 (m) REVERT: A 401 MET cc_start: 0.7674 (pmm) cc_final: 0.7035 (ptp) REVERT: D 252 MET cc_start: 0.9104 (ppp) cc_final: 0.8745 (ppp) REVERT: E 23 PHE cc_start: 0.9248 (t80) cc_final: 0.8981 (t80) REVERT: E 121 LYS cc_start: 0.9179 (pttp) cc_final: 0.8858 (pttm) REVERT: F 137 MET cc_start: 0.7790 (mpp) cc_final: 0.7513 (pmm) outliers start: 16 outliers final: 14 residues processed: 104 average time/residue: 0.2007 time to fit residues: 31.1282 Evaluate side-chains 98 residues out of total 1151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 0 optimal weight: 30.0000 chunk 79 optimal weight: 0.6980 chunk 84 optimal weight: 7.9990 chunk 71 optimal weight: 0.0010 chunk 70 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 overall best weight: 2.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.050806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.040326 restraints weight = 75276.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.041341 restraints weight = 40834.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.042012 restraints weight = 27534.433| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10670 Z= 0.171 Angle : 0.670 11.554 14506 Z= 0.315 Chirality : 0.038 0.205 1691 Planarity : 0.004 0.047 1816 Dihedral : 3.617 22.140 1474 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.51 % Allowed : 22.78 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.24), residues: 1341 helix: 2.09 (0.18), residues: 873 sheet: -1.14 (0.60), residues: 85 loop : -0.98 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 141 HIS 0.004 0.001 HIS D 534 PHE 0.013 0.001 PHE E 42 TYR 0.021 0.001 TYR F 100 ARG 0.003 0.000 ARG F 50 Details of bonding type rmsd hydrogen bonds : bond 0.03816 ( 677) hydrogen bonds : angle 3.74025 ( 2016) covalent geometry : bond 0.00384 (10670) covalent geometry : angle 0.66964 (14506) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3081.28 seconds wall clock time: 54 minutes 21.64 seconds (3261.64 seconds total)