Starting phenix.real_space_refine on Mon Mar 11 06:33:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1k_13163/03_2024/7p1k_13163_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1k_13163/03_2024/7p1k_13163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1k_13163/03_2024/7p1k_13163.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1k_13163/03_2024/7p1k_13163.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1k_13163/03_2024/7p1k_13163_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1k_13163/03_2024/7p1k_13163_trim.pdb" } resolution = 3.64 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 38 5.16 5 C 4648 2.51 5 N 1032 2.21 5 O 1170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6892 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3243 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 19, 'TRANS': 413} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 3243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3243 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 19, 'TRANS': 413} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 203 Unusual residues: {'T7X': 2, 'Y01': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'T7X:plan-1': 1, 'T7X:plan-3': 1, 'T7X:plan-2': 1, 'T7X:plan-5': 1, 'T7X:plan-4': 1, 'T7X:plan-6': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 203 Unusual residues: {'T7X': 2, 'Y01': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'T7X:plan-1': 1, 'T7X:plan-3': 1, 'T7X:plan-2': 1, 'T7X:plan-5': 1, 'T7X:plan-4': 1, 'T7X:plan-6': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 4.16, per 1000 atoms: 0.60 Number of scatterers: 6892 At special positions: 0 Unit cell: (75.0915, 77.121, 118.726, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 4 15.00 O 1170 8.00 N 1032 7.00 C 4648 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 - 3.50 Amino acid : False - 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: 2.82 Conformation dependent library (CDL) restraints added in 1.2 seconds 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1536 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 0 sheets defined 82.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'B' and resid 80 through 104 removed outlier: 3.822A pdb=" N VAL B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 96 " --> pdb=" O MET B 92 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP B 97 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 103 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 134 removed outlier: 3.704A pdb=" N GLY B 116 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE B 117 " --> pdb=" O ASN B 113 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLY B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 158 removed outlier: 4.342A pdb=" N GLY B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 162 removed outlier: 3.811A pdb=" N SER B 162 " --> pdb=" O PRO B 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 159 through 162' Processing helix chain 'B' and resid 168 through 190 removed outlier: 3.523A pdb=" N ILE B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 199 removed outlier: 3.509A pdb=" N LEU B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS B 198 " --> pdb=" O ASN B 194 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 199 " --> pdb=" O ALA B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 226 removed outlier: 3.709A pdb=" N VAL B 204 " --> pdb=" O LYS B 200 " (cutoff:3.500A) Proline residue: B 210 - end of helix Processing helix chain 'B' and resid 229 through 241 removed outlier: 3.573A pdb=" N PHE B 234 " --> pdb=" O TRP B 230 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET B 235 " --> pdb=" O GLN B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 259 removed outlier: 3.922A pdb=" N VAL B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) Proline residue: B 250 - end of helix Processing helix chain 'B' and resid 265 through 276 removed outlier: 3.588A pdb=" N SER B 275 " --> pdb=" O MET B 271 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE B 276 " --> pdb=" O ALA B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 293 removed outlier: 3.665A pdb=" N ALA B 281 " --> pdb=" O ASP B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 319 removed outlier: 3.759A pdb=" N VAL B 309 " --> pdb=" O GLY B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 357 removed outlier: 3.741A pdb=" N ALA B 339 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE B 340 " --> pdb=" O TRP B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 377 removed outlier: 3.869A pdb=" N LEU B 364 " --> pdb=" O GLY B 360 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU B 367 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 404 removed outlier: 3.608A pdb=" N LYS B 386 " --> pdb=" O THR B 382 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 390 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Proline residue: B 397 - end of helix removed outlier: 3.616A pdb=" N PHE B 400 " --> pdb=" O GLN B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 439 removed outlier: 3.572A pdb=" N VAL B 439 " --> pdb=" O THR B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 455 removed outlier: 3.796A pdb=" N ILE B 450 " --> pdb=" O ILE B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 467 removed outlier: 4.048A pdb=" N ALA B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA B 465 " --> pdb=" O THR B 461 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 466 " --> pdb=" O VAL B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 475 Processing helix chain 'B' and resid 480 through 516 removed outlier: 4.179A pdb=" N GLY B 484 " --> pdb=" O LYS B 480 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N TYR B 485 " --> pdb=" O GLN B 481 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA B 501 " --> pdb=" O ILE B 497 " (cutoff:3.500A) Proline residue: B 502 - end of helix removed outlier: 3.560A pdb=" N GLY B 509 " --> pdb=" O SER B 505 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 510 " --> pdb=" O LEU B 506 " (cutoff:3.500A) Proline residue: B 513 - end of helix removed outlier: 3.884A pdb=" N LEU B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 104 removed outlier: 3.792A pdb=" N LEU A 96 " --> pdb=" O MET A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 131 removed outlier: 3.543A pdb=" N ILE A 117 " --> pdb=" O ASN A 113 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 131 " --> pdb=" O GLY A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 158 Processing helix chain 'A' and resid 159 through 162 removed outlier: 3.559A pdb=" N SER A 162 " --> pdb=" O PRO A 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 159 through 162' Processing helix chain 'A' and resid 168 through 190 removed outlier: 3.527A pdb=" N ILE A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 199 removed outlier: 3.620A pdb=" N LEU A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS A 198 " --> pdb=" O ASN A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 226 removed outlier: 3.785A pdb=" N VAL A 204 " --> pdb=" O LYS A 200 " (cutoff:3.500A) Proline residue: A 210 - end of helix Processing helix chain 'A' and resid 229 through 241 removed outlier: 3.698A pdb=" N MET A 235 " --> pdb=" O GLN A 231 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 239 " --> pdb=" O MET A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 259 removed outlier: 3.743A pdb=" N VAL A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) Proline residue: A 250 - end of helix Processing helix chain 'A' and resid 265 through 276 removed outlier: 3.566A pdb=" N SER A 275 " --> pdb=" O MET A 271 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 293 removed outlier: 3.617A pdb=" N ALA A 281 " --> pdb=" O ASP A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 321 removed outlier: 3.691A pdb=" N VAL A 306 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 309 " --> pdb=" O GLY A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 357 removed outlier: 3.500A pdb=" N ALA A 339 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 340 " --> pdb=" O TRP A 336 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 354 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 377 removed outlier: 4.026A pdb=" N LEU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU A 367 " --> pdb=" O GLY A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 404 removed outlier: 3.551A pdb=" N VAL A 384 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS A 386 " --> pdb=" O THR A 382 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Proline residue: A 397 - end of helix removed outlier: 3.605A pdb=" N PHE A 400 " --> pdb=" O GLN A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 438 Processing helix chain 'A' and resid 446 through 455 Processing helix chain 'A' and resid 460 through 466 removed outlier: 4.056A pdb=" N ALA A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 466 " --> pdb=" O VAL A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 477 Processing helix chain 'A' and resid 480 through 516 removed outlier: 3.572A pdb=" N TYR A 485 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 501 " --> pdb=" O ILE A 497 " (cutoff:3.500A) Proline residue: A 502 - end of helix removed outlier: 3.519A pdb=" N LEU A 510 " --> pdb=" O LEU A 506 " (cutoff:3.500A) Proline residue: A 513 - end of helix removed outlier: 3.854A pdb=" N LEU A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) 449 hydrogen bonds defined for protein. 1347 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.78 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1015 1.31 - 1.43: 1725 1.43 - 1.56: 4156 1.56 - 1.68: 104 1.68 - 1.81: 56 Bond restraints: 7056 Sorted by residual: bond pdb=" C21 T7X A 806 " pdb=" C22 T7X A 806 " ideal model delta sigma weight residual 1.329 1.528 -0.199 2.00e-02 2.50e+03 9.86e+01 bond pdb=" C21 T7X B1203 " pdb=" C22 T7X B1203 " ideal model delta sigma weight residual 1.329 1.527 -0.198 2.00e-02 2.50e+03 9.83e+01 bond pdb=" C24 T7X A 806 " pdb=" C25 T7X A 806 " ideal model delta sigma weight residual 1.330 1.527 -0.197 2.00e-02 2.50e+03 9.75e+01 bond pdb=" C24 T7X B1203 " pdb=" C25 T7X B1203 " ideal model delta sigma weight residual 1.330 1.527 -0.197 2.00e-02 2.50e+03 9.73e+01 bond pdb=" C15 T7X B1203 " pdb=" C16 T7X B1203 " ideal model delta sigma weight residual 1.332 1.528 -0.196 2.00e-02 2.50e+03 9.62e+01 ... (remaining 7051 not shown) Histogram of bond angle deviations from ideal: 94.74 - 102.59: 49 102.59 - 110.45: 1893 110.45 - 118.30: 3868 118.30 - 126.15: 3725 126.15 - 134.01: 111 Bond angle restraints: 9646 Sorted by residual: angle pdb=" O11 T7X B1203 " pdb=" P1 T7X B1203 " pdb=" O12 T7X B1203 " ideal model delta sigma weight residual 119.68 100.92 18.76 3.00e+00 1.11e-01 3.91e+01 angle pdb=" O11 T7X A 806 " pdb=" P1 T7X A 806 " pdb=" O12 T7X A 806 " ideal model delta sigma weight residual 119.68 101.10 18.58 3.00e+00 1.11e-01 3.84e+01 angle pdb=" N ASP B 163 " pdb=" CA ASP B 163 " pdb=" C ASP B 163 " ideal model delta sigma weight residual 114.31 106.98 7.33 1.29e+00 6.01e-01 3.23e+01 angle pdb=" O1 T7X B1203 " pdb=" P1 T7X B1203 " pdb=" O13 T7X B1203 " ideal model delta sigma weight residual 94.60 110.62 -16.02 3.00e+00 1.11e-01 2.85e+01 angle pdb=" N TRP B 171 " pdb=" CA TRP B 171 " pdb=" C TRP B 171 " ideal model delta sigma weight residual 113.50 107.07 6.43 1.23e+00 6.61e-01 2.73e+01 ... (remaining 9641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.56: 4460 35.56 - 71.11: 92 71.11 - 106.67: 13 106.67 - 142.22: 6 142.22 - 177.78: 7 Dihedral angle restraints: 4578 sinusoidal: 2166 harmonic: 2412 Sorted by residual: dihedral pdb=" C7 T7X A 806 " pdb=" O13 T7X A 806 " pdb=" P1 T7X A 806 " pdb=" O12 T7X A 806 " ideal model delta sinusoidal sigma weight residual 91.36 -90.86 -177.78 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C7 T7X B1203 " pdb=" O13 T7X B1203 " pdb=" P1 T7X B1203 " pdb=" O11 T7X B1203 " ideal model delta sinusoidal sigma weight residual 318.06 147.62 170.44 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C7 T7X B1203 " pdb=" O13 T7X B1203 " pdb=" P1 T7X B1203 " pdb=" O12 T7X B1203 " ideal model delta sinusoidal sigma weight residual 91.36 -100.83 -167.81 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 4575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1112 0.074 - 0.148: 59 0.148 - 0.222: 23 0.222 - 0.296: 2 0.296 - 0.370: 8 Chirality restraints: 1204 Sorted by residual: chirality pdb=" CBG Y01 A 804 " pdb=" CAQ Y01 A 804 " pdb=" CBD Y01 A 804 " pdb=" CBI Y01 A 804 " both_signs ideal model delta sigma weight residual False -2.33 -2.70 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CBG Y01 B1201 " pdb=" CAQ Y01 B1201 " pdb=" CBD Y01 B1201 " pdb=" CBI Y01 B1201 " both_signs ideal model delta sigma weight residual False -2.33 -2.70 0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CBG Y01 A 803 " pdb=" CAQ Y01 A 803 " pdb=" CBD Y01 A 803 " pdb=" CBI Y01 A 803 " both_signs ideal model delta sigma weight residual False -2.33 -2.69 0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 1201 not shown) Planarity restraints: 1118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 T7X A 806 " 0.135 2.00e-02 2.50e+03 3.42e-01 1.17e+03 pdb=" C18 T7X A 806 " -0.438 2.00e-02 2.50e+03 pdb=" C19 T7X A 806 " 0.476 2.00e-02 2.50e+03 pdb=" C20 T7X A 806 " -0.173 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 T7X A 806 " 0.150 2.00e-02 2.50e+03 3.31e-01 1.10e+03 pdb=" C24 T7X A 806 " -0.437 2.00e-02 2.50e+03 pdb=" C25 T7X A 806 " 0.447 2.00e-02 2.50e+03 pdb=" C26 T7X A 806 " -0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 T7X B1203 " -0.152 2.00e-02 2.50e+03 3.11e-01 9.67e+02 pdb=" C24 T7X B1203 " 0.410 2.00e-02 2.50e+03 pdb=" C25 T7X B1203 " -0.414 2.00e-02 2.50e+03 pdb=" C26 T7X B1203 " 0.156 2.00e-02 2.50e+03 ... (remaining 1115 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 52 2.60 - 3.17: 6088 3.17 - 3.75: 10006 3.75 - 4.32: 13397 4.32 - 4.90: 22515 Nonbonded interactions: 52058 Sorted by model distance: nonbonded pdb=" N GLU A 385 " pdb=" OE1 GLU A 385 " model vdw 2.023 2.520 nonbonded pdb=" O PHE A 153 " pdb=" ND2 ASN A 157 " model vdw 2.200 2.520 nonbonded pdb=" O PHE B 153 " pdb=" ND2 ASN B 157 " model vdw 2.231 2.520 nonbonded pdb=" O PHE B 444 " pdb=" NZ LYS B 449 " model vdw 2.238 2.520 nonbonded pdb=" O VAL B 239 " pdb=" NE2 GLN B 463 " model vdw 2.304 2.520 ... (remaining 52053 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 79 through 517 or resid 801 or resid 804)) selection = (chain 'B' and (resid 79 through 517 or resid 1201 or resid 1204)) } 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: 0.690 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: 3.940 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.090 Find NCS groups from input model: 0.410 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: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 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 : 0.014 0.199 7056 Z= 0.885 Angle : 1.119 18.761 9646 Z= 0.459 Chirality : 0.053 0.370 1204 Planarity : 0.024 0.342 1118 Dihedral : 16.196 177.778 3042 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.61 % Allowed : 7.93 % Favored : 87.46 % 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: -0.19 (0.29), residues: 858 helix: 0.60 (0.20), residues: 632 sheet: None (None), residues: 0 loop : -2.10 (0.46), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 171 HIS 0.002 0.001 HIS A 169 PHE 0.005 0.001 PHE A 300 TYR 0.005 0.001 TYR A 260 ARG 0.002 0.000 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 209 time to evaluate : 0.711 Fit side-chains TARDY: cannot create tardy model for: "CYS B 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 108 " (corrupted residue). Skipping it. REVERT: B 200 LYS cc_start: 0.7652 (mtmt) cc_final: 0.7014 (mmtt) REVERT: B 226 MET cc_start: 0.6218 (mmt) cc_final: 0.5976 (mpp) REVERT: B 346 SER cc_start: 0.7929 (t) cc_final: 0.7726 (m) REVERT: B 426 ILE cc_start: 0.8581 (mt) cc_final: 0.8376 (mm) REVERT: B 438 MET cc_start: 0.7032 (mmm) cc_final: 0.6743 (mmt) REVERT: B 507 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7748 (mt) REVERT: A 86 VAL cc_start: 0.6782 (m) cc_final: 0.6572 (t) REVERT: A 96 LEU cc_start: 0.8448 (tt) cc_final: 0.8126 (tp) REVERT: A 165 ILE cc_start: 0.7289 (OUTLIER) cc_final: 0.6990 (mt) REVERT: A 396 GLN cc_start: 0.8563 (tp40) cc_final: 0.7648 (tt0) outliers start: 32 outliers final: 9 residues processed: 231 average time/residue: 0.2114 time to fit residues: 62.6623 Evaluate side-chains 157 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 146 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 300 PHE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 459 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 0.0170 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 26 optimal weight: 0.6980 chunk 40 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN B 286 ASN B 333 ASN B 477 HIS A 113 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7056 Z= 0.200 Angle : 0.709 8.933 9646 Z= 0.336 Chirality : 0.040 0.138 1204 Planarity : 0.005 0.045 1118 Dihedral : 16.678 176.113 1661 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.89 % Allowed : 14.70 % Favored : 81.41 % 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: 1.19 (0.30), residues: 858 helix: 1.75 (0.20), residues: 632 sheet: None (None), residues: 0 loop : -2.11 (0.45), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 171 HIS 0.002 0.001 HIS B 169 PHE 0.012 0.001 PHE A 238 TYR 0.010 0.001 TYR A 223 ARG 0.004 0.001 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 154 time to evaluate : 0.697 Fit side-chains TARDY: cannot create tardy model for: "CYS B 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 108 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 200 LYS cc_start: 0.7587 (mtmt) cc_final: 0.6789 (mmtt) REVERT: B 358 PHE cc_start: 0.6681 (OUTLIER) cc_final: 0.5637 (p90) REVERT: B 375 ARG cc_start: 0.6760 (mtp85) cc_final: 0.6547 (ttt-90) REVERT: B 436 TYR cc_start: 0.7875 (t80) cc_final: 0.7490 (t80) REVERT: B 483 GLU cc_start: 0.6681 (mm-30) cc_final: 0.6474 (mm-30) REVERT: A 96 LEU cc_start: 0.7907 (tt) cc_final: 0.7644 (tp) REVERT: A 153 PHE cc_start: 0.6578 (t80) cc_final: 0.6256 (t80) REVERT: A 165 ILE cc_start: 0.7298 (OUTLIER) cc_final: 0.6968 (mt) REVERT: A 323 ILE cc_start: 0.8269 (mt) cc_final: 0.8016 (mm) REVERT: A 396 GLN cc_start: 0.8597 (tp-100) cc_final: 0.7726 (tt0) REVERT: A 412 LEU cc_start: 0.1264 (OUTLIER) cc_final: 0.1048 (mm) REVERT: A 495 LEU cc_start: 0.7406 (mt) cc_final: 0.7161 (mt) outliers start: 27 outliers final: 17 residues processed: 171 average time/residue: 0.1898 time to fit residues: 42.7325 Evaluate side-chains 155 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 301 ASN Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 500 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 64 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 78 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 ASN A 157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7056 Z= 0.164 Angle : 0.626 8.960 9646 Z= 0.294 Chirality : 0.039 0.177 1204 Planarity : 0.004 0.040 1118 Dihedral : 14.934 178.722 1655 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 5.04 % Allowed : 14.70 % Favored : 80.26 % 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 (0.30), residues: 858 helix: 2.01 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.13 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 392 HIS 0.005 0.001 HIS B 477 PHE 0.010 0.001 PHE A 494 TYR 0.013 0.001 TYR B 223 ARG 0.004 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 138 time to evaluate : 0.655 Fit side-chains TARDY: cannot create tardy model for: "CYS B 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 108 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 82 LEU cc_start: 0.5063 (OUTLIER) cc_final: 0.4768 (tp) REVERT: B 200 LYS cc_start: 0.7589 (mtmt) cc_final: 0.6661 (mmtt) REVERT: B 266 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7341 (mp) REVERT: B 358 PHE cc_start: 0.6656 (OUTLIER) cc_final: 0.5505 (p90) REVERT: B 507 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7654 (mt) REVERT: A 165 ILE cc_start: 0.7221 (OUTLIER) cc_final: 0.6680 (mt) REVERT: A 396 GLN cc_start: 0.8501 (tp-100) cc_final: 0.7696 (tt0) REVERT: A 412 LEU cc_start: 0.1337 (OUTLIER) cc_final: 0.1051 (mm) REVERT: A 495 LEU cc_start: 0.7505 (mt) cc_final: 0.7300 (mt) REVERT: A 510 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6359 (pt) outliers start: 35 outliers final: 21 residues processed: 165 average time/residue: 0.1829 time to fit residues: 39.7128 Evaluate side-chains 155 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 127 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 301 ASN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 510 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 ASN ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7056 Z= 0.290 Angle : 0.712 9.088 9646 Z= 0.337 Chirality : 0.042 0.198 1204 Planarity : 0.005 0.041 1118 Dihedral : 14.190 177.593 1655 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 5.62 % Allowed : 16.14 % Favored : 78.24 % 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: 1.08 (0.29), residues: 858 helix: 1.66 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -2.21 (0.46), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 232 HIS 0.007 0.002 HIS B 477 PHE 0.013 0.002 PHE A 153 TYR 0.010 0.002 TYR B 260 ARG 0.005 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 123 time to evaluate : 0.684 Fit side-chains TARDY: cannot create tardy model for: "CYS B 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 108 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 103 VAL cc_start: 0.7845 (OUTLIER) cc_final: 0.7526 (t) REVERT: B 266 ILE cc_start: 0.7712 (OUTLIER) cc_final: 0.7482 (mp) REVERT: B 279 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.7847 (mp) REVERT: B 358 PHE cc_start: 0.6866 (OUTLIER) cc_final: 0.5630 (p90) REVERT: B 475 ARG cc_start: 0.7685 (ttm110) cc_final: 0.7397 (ptp-110) REVERT: B 477 HIS cc_start: 0.5969 (m-70) cc_final: 0.5321 (m-70) REVERT: B 507 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7719 (mt) REVERT: A 165 ILE cc_start: 0.7315 (OUTLIER) cc_final: 0.7063 (mt) REVERT: A 396 GLN cc_start: 0.8539 (tp-100) cc_final: 0.7686 (tt0) REVERT: A 495 LEU cc_start: 0.7542 (mt) cc_final: 0.7316 (mt) REVERT: A 510 LEU cc_start: 0.6658 (OUTLIER) cc_final: 0.6407 (pt) outliers start: 39 outliers final: 24 residues processed: 150 average time/residue: 0.1816 time to fit residues: 36.4929 Evaluate side-chains 154 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 123 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 301 ASN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 510 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7056 Z= 0.162 Angle : 0.597 6.100 9646 Z= 0.284 Chirality : 0.038 0.136 1204 Planarity : 0.004 0.041 1118 Dihedral : 13.208 178.183 1653 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 5.62 % Allowed : 15.85 % Favored : 78.53 % 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: 1.49 (0.30), residues: 858 helix: 1.98 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -2.14 (0.45), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 97 HIS 0.004 0.001 HIS B 477 PHE 0.010 0.001 PHE A 494 TYR 0.007 0.001 TYR A 260 ARG 0.004 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 130 time to evaluate : 0.738 Fit side-chains TARDY: cannot create tardy model for: "CYS B 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 108 " (corrupted residue). Skipping it. REVERT: B 82 LEU cc_start: 0.5460 (OUTLIER) cc_final: 0.5150 (tp) REVERT: B 119 MET cc_start: 0.6657 (OUTLIER) cc_final: 0.6429 (mmp) REVERT: B 279 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.7708 (mp) REVERT: B 358 PHE cc_start: 0.6739 (OUTLIER) cc_final: 0.5530 (p90) REVERT: B 448 GLU cc_start: 0.6539 (mm-30) cc_final: 0.6256 (mm-30) REVERT: B 456 TRP cc_start: 0.7984 (OUTLIER) cc_final: 0.6704 (m-90) REVERT: B 475 ARG cc_start: 0.7702 (ttm110) cc_final: 0.7416 (ptp-110) REVERT: B 477 HIS cc_start: 0.5968 (m-70) cc_final: 0.5256 (m-70) REVERT: B 507 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7622 (mt) REVERT: A 165 ILE cc_start: 0.7291 (OUTLIER) cc_final: 0.6963 (mt) REVERT: A 396 GLN cc_start: 0.8492 (tp-100) cc_final: 0.7671 (tt0) REVERT: A 510 LEU cc_start: 0.6633 (OUTLIER) cc_final: 0.6366 (pt) outliers start: 39 outliers final: 22 residues processed: 154 average time/residue: 0.1809 time to fit residues: 37.3265 Evaluate side-chains 154 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 124 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 516 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.1980 chunk 74 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 48 optimal weight: 0.0980 chunk 20 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 69 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 0.0020 chunk 43 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 463 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7056 Z= 0.141 Angle : 0.576 7.626 9646 Z= 0.274 Chirality : 0.038 0.163 1204 Planarity : 0.004 0.037 1118 Dihedral : 12.491 179.769 1647 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.76 % Allowed : 16.57 % Favored : 78.67 % 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: 1.75 (0.30), residues: 858 helix: 2.17 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -2.07 (0.46), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 97 HIS 0.003 0.001 HIS B 477 PHE 0.013 0.001 PHE A 153 TYR 0.019 0.001 TYR A 485 ARG 0.006 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 131 time to evaluate : 0.772 Fit side-chains TARDY: cannot create tardy model for: "CYS B 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 108 " (corrupted residue). Skipping it. REVERT: B 82 LEU cc_start: 0.5432 (OUTLIER) cc_final: 0.5113 (tp) REVERT: B 223 TYR cc_start: 0.7507 (t80) cc_final: 0.7226 (t80) REVERT: B 286 ASN cc_start: 0.7468 (m110) cc_final: 0.7211 (m110) REVERT: B 358 PHE cc_start: 0.6634 (OUTLIER) cc_final: 0.5418 (p90) REVERT: B 448 GLU cc_start: 0.6525 (mm-30) cc_final: 0.6289 (mm-30) REVERT: B 456 TRP cc_start: 0.7958 (OUTLIER) cc_final: 0.6728 (m-90) REVERT: B 475 ARG cc_start: 0.7661 (ttm110) cc_final: 0.7370 (ptp-110) REVERT: B 477 HIS cc_start: 0.5848 (m-70) cc_final: 0.5202 (m-70) REVERT: B 507 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7573 (mt) REVERT: A 165 ILE cc_start: 0.7218 (OUTLIER) cc_final: 0.6648 (mt) REVERT: A 291 MET cc_start: 0.5471 (mmp) cc_final: 0.5060 (mtt) REVERT: A 396 GLN cc_start: 0.8434 (tp-100) cc_final: 0.7635 (tt0) REVERT: A 510 LEU cc_start: 0.6537 (OUTLIER) cc_final: 0.6260 (pt) outliers start: 33 outliers final: 18 residues processed: 152 average time/residue: 0.1855 time to fit residues: 37.5417 Evaluate side-chains 148 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 124 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 301 ASN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 516 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 60 optimal weight: 0.0980 chunk 70 optimal weight: 0.7980 chunk 46 optimal weight: 0.4980 chunk 82 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 38 optimal weight: 0.0570 chunk 33 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 481 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7056 Z= 0.147 Angle : 0.571 6.339 9646 Z= 0.274 Chirality : 0.038 0.210 1204 Planarity : 0.004 0.037 1118 Dihedral : 12.190 179.366 1647 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.18 % Allowed : 17.15 % Favored : 78.67 % 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: 1.80 (0.30), residues: 858 helix: 2.19 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -2.01 (0.47), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 97 HIS 0.003 0.001 HIS B 477 PHE 0.015 0.001 PHE A 494 TYR 0.008 0.001 TYR A 223 ARG 0.005 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 130 time to evaluate : 0.740 Fit side-chains TARDY: cannot create tardy model for: "CYS B 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 108 " (corrupted residue). Skipping it. REVERT: B 82 LEU cc_start: 0.5449 (OUTLIER) cc_final: 0.5033 (tp) REVERT: B 85 ARG cc_start: 0.6081 (ptt180) cc_final: 0.5628 (ttp-170) REVERT: B 223 TYR cc_start: 0.7447 (t80) cc_final: 0.7217 (t80) REVERT: B 358 PHE cc_start: 0.6645 (OUTLIER) cc_final: 0.5360 (p90) REVERT: B 456 TRP cc_start: 0.7925 (OUTLIER) cc_final: 0.6727 (m-90) REVERT: B 475 ARG cc_start: 0.7634 (ttm110) cc_final: 0.7309 (ptp-110) REVERT: B 477 HIS cc_start: 0.5866 (m-70) cc_final: 0.5223 (m-70) REVERT: A 291 MET cc_start: 0.5446 (mmp) cc_final: 0.5036 (mtt) REVERT: A 396 GLN cc_start: 0.8411 (tp-100) cc_final: 0.7621 (tt0) REVERT: A 510 LEU cc_start: 0.6589 (OUTLIER) cc_final: 0.6354 (pt) outliers start: 29 outliers final: 20 residues processed: 149 average time/residue: 0.1765 time to fit residues: 35.2823 Evaluate side-chains 148 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 124 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 301 ASN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 510 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7056 Z= 0.175 Angle : 0.591 8.503 9646 Z= 0.283 Chirality : 0.038 0.174 1204 Planarity : 0.004 0.033 1118 Dihedral : 12.059 179.125 1647 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.32 % Allowed : 18.16 % Favored : 77.52 % 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: 1.74 (0.30), residues: 858 helix: 2.11 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -2.03 (0.48), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 392 HIS 0.004 0.001 HIS B 477 PHE 0.017 0.001 PHE A 494 TYR 0.007 0.001 TYR B 260 ARG 0.006 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 125 time to evaluate : 0.687 Fit side-chains TARDY: cannot create tardy model for: "CYS B 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 108 " (corrupted residue). Skipping it. REVERT: B 82 LEU cc_start: 0.5457 (OUTLIER) cc_final: 0.5028 (tp) REVERT: B 85 ARG cc_start: 0.6084 (ptt180) cc_final: 0.5616 (ttp-170) REVERT: B 358 PHE cc_start: 0.6616 (OUTLIER) cc_final: 0.5453 (p90) REVERT: B 456 TRP cc_start: 0.7983 (OUTLIER) cc_final: 0.6760 (m-90) REVERT: B 475 ARG cc_start: 0.7683 (ttm110) cc_final: 0.7401 (ptp-110) REVERT: B 477 HIS cc_start: 0.5820 (m-70) cc_final: 0.5223 (m-70) REVERT: A 291 MET cc_start: 0.5523 (mmp) cc_final: 0.5088 (mtt) REVERT: A 364 LEU cc_start: 0.6970 (pp) cc_final: 0.6629 (tp) REVERT: A 396 GLN cc_start: 0.8434 (tp-100) cc_final: 0.7647 (tt0) REVERT: A 510 LEU cc_start: 0.6643 (OUTLIER) cc_final: 0.6408 (pt) outliers start: 30 outliers final: 21 residues processed: 146 average time/residue: 0.1826 time to fit residues: 35.7384 Evaluate side-chains 148 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 123 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 510 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7056 Z= 0.211 Angle : 0.617 6.695 9646 Z= 0.298 Chirality : 0.040 0.164 1204 Planarity : 0.004 0.034 1118 Dihedral : 12.045 178.154 1647 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.03 % Allowed : 18.16 % Favored : 77.81 % 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: 1.55 (0.30), residues: 858 helix: 1.98 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -2.09 (0.48), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 232 HIS 0.004 0.001 HIS B 477 PHE 0.015 0.001 PHE A 494 TYR 0.015 0.001 TYR B 223 ARG 0.006 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 128 time to evaluate : 0.744 Fit side-chains TARDY: cannot create tardy model for: "CYS B 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 108 " (corrupted residue). Skipping it. REVERT: B 82 LEU cc_start: 0.5488 (OUTLIER) cc_final: 0.5152 (tp) REVERT: B 358 PHE cc_start: 0.6786 (OUTLIER) cc_final: 0.5521 (p90) REVERT: B 456 TRP cc_start: 0.8013 (OUTLIER) cc_final: 0.6751 (m-90) REVERT: B 475 ARG cc_start: 0.7725 (ttm110) cc_final: 0.7506 (ptp-110) REVERT: A 155 ILE cc_start: 0.8148 (mm) cc_final: 0.7923 (mt) REVERT: A 291 MET cc_start: 0.5608 (mmp) cc_final: 0.5179 (mtt) REVERT: A 364 LEU cc_start: 0.6993 (pp) cc_final: 0.6623 (tp) REVERT: A 396 GLN cc_start: 0.8429 (tp-100) cc_final: 0.7634 (tt0) REVERT: A 510 LEU cc_start: 0.6574 (OUTLIER) cc_final: 0.6336 (pt) outliers start: 28 outliers final: 24 residues processed: 148 average time/residue: 0.1797 time to fit residues: 35.6971 Evaluate side-chains 152 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 124 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 516 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 85 optimal weight: 0.3980 chunk 78 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 72 optimal weight: 0.2980 chunk 20 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 ASN A 481 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7056 Z= 0.155 Angle : 0.592 8.057 9646 Z= 0.284 Chirality : 0.038 0.166 1204 Planarity : 0.004 0.032 1118 Dihedral : 11.835 177.537 1647 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.89 % Allowed : 19.16 % Favored : 76.95 % 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: 1.75 (0.30), residues: 858 helix: 2.13 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -2.03 (0.48), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 97 HIS 0.002 0.001 HIS B 477 PHE 0.015 0.001 PHE A 494 TYR 0.007 0.001 TYR B 260 ARG 0.005 0.000 ARG A 156 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 122 time to evaluate : 0.762 Fit side-chains TARDY: cannot create tardy model for: "CYS B 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS A 108 " (corrupted residue). Skipping it. REVERT: B 82 LEU cc_start: 0.5462 (OUTLIER) cc_final: 0.5155 (tp) REVERT: B 358 PHE cc_start: 0.6733 (OUTLIER) cc_final: 0.5496 (p90) REVERT: B 456 TRP cc_start: 0.7973 (OUTLIER) cc_final: 0.6752 (m-90) REVERT: B 475 ARG cc_start: 0.7747 (ttm110) cc_final: 0.7528 (ptp-110) REVERT: A 165 ILE cc_start: 0.7141 (OUTLIER) cc_final: 0.6599 (mt) REVERT: A 291 MET cc_start: 0.5540 (mmp) cc_final: 0.5111 (mtt) REVERT: A 396 GLN cc_start: 0.8369 (tp-100) cc_final: 0.7578 (tt0) REVERT: A 510 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.6401 (pt) outliers start: 27 outliers final: 20 residues processed: 142 average time/residue: 0.1825 time to fit residues: 35.0087 Evaluate side-chains 144 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 456 TRP Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 516 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 59 optimal weight: 0.2980 chunk 3 optimal weight: 0.0070 chunk 49 optimal weight: 0.0570 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.208808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.177542 restraints weight = 7497.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.173832 restraints weight = 11943.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.175800 restraints weight = 12272.543| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7056 Z= 0.143 Angle : 0.566 6.879 9646 Z= 0.274 Chirality : 0.037 0.171 1204 Planarity : 0.004 0.033 1118 Dihedral : 11.582 177.624 1647 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.59 % Allowed : 20.32 % Favored : 77.09 % 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: 1.89 (0.30), residues: 858 helix: 2.23 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -2.00 (0.48), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 97 HIS 0.001 0.000 HIS B 477 PHE 0.014 0.001 PHE A 494 TYR 0.007 0.001 TYR A 485 ARG 0.004 0.000 ARG A 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1558.78 seconds wall clock time: 28 minutes 54.48 seconds (1734.48 seconds total)