Starting phenix.real_space_refine on Thu Jul 2 11:39:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7d9u_30621/07_2026/7d9u_30621.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d9u_30621/07_2026/7d9u_30621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d9u_30621/07_2026/7d9u_30621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d9u_30621/07_2026/7d9u_30621.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7d9u_30621/07_2026/7d9u_30621.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7d9u_30621/07_2026/7d9u_30621.cif" model { file = "/net/cci-nas-00/data/ceres_data/7d9u_30621/07_2026/7d9u_30621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d9u_30621/07_2026/7d9u_30621.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 5264 2.51 5 N 1389 2.21 5 O 1476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8190 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3742 Classifications: {'peptide': 506} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 23, 'TRANS': 482} Chain breaks: 8 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 216 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 16, 'ASN:plan1': 1, 'GLN:plan1': 2, 'ARG:plan': 6, 'TYR:plan': 1, 'ASP:plan': 7, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 162 Chain: "B" Number of atoms: 4372 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 569, 4368 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 545} Chain breaks: 3 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 148 Planarities with less than four sites: {'GLU:plan': 20, 'ASP:plan': 7, 'GLN:plan1': 3, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 138 Conformer: "B" Number of residues, atoms: 569, 4368 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 545} Chain breaks: 3 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 148 Planarities with less than four sites: {'GLU:plan': 20, 'ASP:plan': 7, 'GLN:plan1': 3, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 138 bond proxies already assigned to first conformer: 4452 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 2, 'G2P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'Z90': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LEU A 254 " occ=0.92 ... (3 atoms not shown) pdb=" CB LEU A 254 " occ=0.92 Time building chain proxies: 2.44, per 1000 atoms: 0.30 Number of scatterers: 8190 At special positions: 0 Unit cell: (99.275, 137.94, 137.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 3 15.00 Mg 2 11.99 O 1476 8.00 N 1389 7.00 C 5264 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: 0.87 Conformation dependent library (CDL) restraints added in 490.0 milliseconds 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2026 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 11 sheets defined 49.6% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 70 through 83 Processing helix chain 'A' and resid 85 through 101 Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 128 through 146 Processing helix chain 'A' and resid 158 through 171 removed outlier: 3.892A pdb=" N PHE A 166 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N SER A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 226 Processing helix chain 'A' and resid 278 through 286 Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 334 through 341 Processing helix chain 'A' and resid 399 through 403 Processing helix chain 'A' and resid 408 through 458 removed outlier: 3.853A pdb=" N VAL A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 468 removed outlier: 4.240A pdb=" N GLN A 468 " --> pdb=" O GLN A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 497 removed outlier: 3.637A pdb=" N ILE A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 519 removed outlier: 3.699A pdb=" N GLU A 519 " --> pdb=" O GLN A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 561 Processing helix chain 'A' and resid 598 through 610 removed outlier: 3.884A pdb=" N THR A 602 " --> pdb=" O GLY A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 627 Processing helix chain 'B' and resid 2 through 29 removed outlier: 4.084A pdb=" N ASN B 6 " --> pdb=" O TYR B 2 " (cutoff:3.500A) Proline residue: B 19 - end of helix removed outlier: 3.820A pdb=" N TRP B 22 " --> pdb=" O GLY B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.803A pdb=" N THR B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 82 removed outlier: 3.699A pdb=" N ILE B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 90 removed outlier: 3.850A pdb=" N LEU B 87 " --> pdb=" O TYR B 83 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 90 " --> pdb=" O ILE B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 112 removed outlier: 4.597A pdb=" N ASP B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ALA B 103 " --> pdb=" O GLN B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 158 removed outlier: 3.774A pdb=" N ILE B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 217 Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 249 through 253 removed outlier: 3.865A pdb=" N VAL B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 249 through 253' Processing helix chain 'B' and resid 264 through 271 Processing helix chain 'B' and resid 282 through 285 removed outlier: 4.365A pdb=" N LEU B 285 " --> pdb=" O GLU B 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 282 through 285' Processing helix chain 'B' and resid 329 through 335 removed outlier: 3.668A pdb=" N LEU B 333 " --> pdb=" O ASN B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 343 Processing helix chain 'B' and resid 348 through 398 removed outlier: 4.393A pdb=" N LEU B 354 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 408 removed outlier: 4.247A pdb=" N HIS B 408 " --> pdb=" O ASN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 437 Processing helix chain 'B' and resid 443 through 461 Processing helix chain 'B' and resid 491 through 507 removed outlier: 3.848A pdb=" N SER B 495 " --> pdb=" O HIS B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 557 removed outlier: 3.710A pdb=" N ASN B 548 " --> pdb=" O GLY B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 574 removed outlier: 3.917A pdb=" N SER B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 234 Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 300 removed outlier: 6.405A pdb=" N MET A 291 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE A 290 " --> pdb=" O PHE A 381 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 292 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY A 368 " --> pdb=" O PHE A 346 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 523 through 525 removed outlier: 4.296A pdb=" N CYS A 533 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 481 " --> pdb=" O GLY A 536 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 484 " --> pdb=" O GLY A 576 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 583 through 585 Processing sheet with id=AA5, first strand: chain 'B' and resid 119 through 124 removed outlier: 3.617A pdb=" N ARG B 121 " --> pdb=" O HIS B 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 162 through 164 removed outlier: 3.941A pdb=" N ASP B 163 " --> pdb=" O GLU B 182 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU B 182 " --> pdb=" O ASP B 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 231 removed outlier: 3.658A pdb=" N PHE B 223 " --> pdb=" O ILE B 319 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 319 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL B 277 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 415 through 417 removed outlier: 3.686A pdb=" N GLY B 531 " --> pdb=" O CYS B 541 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS B 541 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 478 through 479 removed outlier: 3.591A pdb=" N ILE B 422 " --> pdb=" O HIS B 524 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS B 524 " --> pdb=" O ILE B 422 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ASN B 563 " --> pdb=" O ILE B 519 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ILE B 521 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N SER B 565 " --> pdb=" O ILE B 521 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE B 523 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N MET B 599 " --> pdb=" O PRO B 589 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL B 601 " --> pdb=" O ARG B 587 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 469 through 470 Processing sheet with id=AB2, first strand: chain 'B' and resid 511 through 512 441 hydrogen bonds defined for protein. 1260 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: 1.45 Time building geometry restraints manager: 1.09 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: 2635 1.34 - 1.46: 1766 1.46 - 1.58: 3858 1.58 - 1.69: 5 1.69 - 1.81: 86 Bond restraints: 8350 Sorted by residual: bond pdb=" O3B G2P A1001 " pdb=" PG G2P A1001 " ideal model delta sigma weight residual 1.716 1.606 0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" O1A G2P A1001 " pdb=" PA G2P A1001 " ideal model delta sigma weight residual 1.507 1.608 -0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" O1B G2P A1001 " pdb=" PB G2P A1001 " ideal model delta sigma weight residual 1.510 1.608 -0.098 2.00e-02 2.50e+03 2.43e+01 bond pdb=" C4 G2P A1001 " pdb=" C5 G2P A1001 " ideal model delta sigma weight residual 1.384 1.467 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" CBN Z90 B 701 " pdb=" CBO Z90 B 701 " ideal model delta sigma weight residual 1.405 1.480 -0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 8345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 11226 2.26 - 4.52: 94 4.52 - 6.77: 12 6.77 - 9.03: 7 9.03 - 11.29: 4 Bond angle restraints: 11343 Sorted by residual: angle pdb=" C3A G2P A1001 " pdb=" PB G2P A1001 " pdb=" O3B G2P A1001 " ideal model delta sigma weight residual 99.71 111.00 -11.29 3.00e+00 1.11e-01 1.42e+01 angle pdb=" PA G2P A1001 " pdb=" C3A G2P A1001 " pdb=" PB G2P A1001 " ideal model delta sigma weight residual 120.83 110.32 10.51 3.00e+00 1.11e-01 1.23e+01 angle pdb=" C3A G2P A1001 " pdb=" PA G2P A1001 " pdb=" O5' G2P A1001 " ideal model delta sigma weight residual 99.14 109.41 -10.27 3.00e+00 1.11e-01 1.17e+01 angle pdb=" C5 G2P A1001 " pdb=" C4 G2P A1001 " pdb=" N3 G2P A1001 " ideal model delta sigma weight residual 128.08 118.68 9.40 3.00e+00 1.11e-01 9.81e+00 angle pdb=" N3 G2P A1001 " pdb=" C4 G2P A1001 " pdb=" N9 G2P A1001 " ideal model delta sigma weight residual 126.73 134.95 -8.22 3.00e+00 1.11e-01 7.51e+00 ... (remaining 11338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.93: 4811 24.93 - 49.86: 148 49.86 - 74.80: 10 74.80 - 99.73: 1 99.73 - 124.66: 2 Dihedral angle restraints: 4972 sinusoidal: 1849 harmonic: 3123 Sorted by residual: dihedral pdb=" CAX Z90 B 701 " pdb=" CAV Z90 B 701 " pdb=" CAW Z90 B 701 " pdb=" CBB Z90 B 701 " ideal model delta sinusoidal sigma weight residual 179.41 -55.93 -124.66 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" CAW Z90 B 701 " pdb=" CBB Z90 B 701 " pdb=" NBP Z90 B 701 " pdb=" CBC Z90 B 701 " ideal model delta sinusoidal sigma weight residual -158.43 -36.24 -122.19 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" CA LEU B 338 " pdb=" C LEU B 338 " pdb=" N TYR B 339 " pdb=" CA TYR B 339 " ideal model delta harmonic sigma weight residual 180.00 164.21 15.79 0 5.00e+00 4.00e-02 9.97e+00 ... (remaining 4969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 875 0.032 - 0.063: 316 0.063 - 0.095: 101 0.095 - 0.127: 46 0.127 - 0.158: 4 Chirality restraints: 1342 Sorted by residual: chirality pdb=" C1' G2P A1001 " pdb=" C2' G2P A1001 " pdb=" N9 G2P A1001 " pdb=" O4' G2P A1001 " both_signs ideal model delta sigma weight residual False 2.36 2.52 -0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CA PRO B 210 " pdb=" N PRO B 210 " pdb=" C PRO B 210 " pdb=" CB PRO B 210 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" C2' G2P A1001 " pdb=" C1' G2P A1001 " pdb=" C3' G2P A1001 " pdb=" O2' G2P A1001 " both_signs ideal model delta sigma weight residual False -2.48 -2.62 0.14 2.00e-01 2.50e+01 5.01e-01 ... (remaining 1339 not shown) Planarity restraints: 1431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 565 " -0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO A 566 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 566 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 566 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 485 " 0.005 2.00e-02 2.50e+03 1.09e-02 1.19e+00 pdb=" C SER A 485 " -0.019 2.00e-02 2.50e+03 pdb=" O SER A 485 " 0.007 2.00e-02 2.50e+03 pdb=" N ASP A 486 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 642 " 0.018 5.00e-02 4.00e+02 2.72e-02 1.19e+00 pdb=" N PRO A 643 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 643 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 643 " 0.015 5.00e-02 4.00e+02 ... (remaining 1428 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 499 2.73 - 3.27: 8569 3.27 - 3.81: 13433 3.81 - 4.36: 15179 4.36 - 4.90: 26681 Nonbonded interactions: 64361 Sorted by model distance: nonbonded pdb=" O1A G2P A1001 " pdb=" O3B G2P A1001 " model vdw 2.187 3.040 nonbonded pdb=" OG SER B 280 " pdb=" O CYS B 303 " model vdw 2.213 3.040 nonbonded pdb=" O LEU A 520 " pdb=" NE2 GLN A 548 " model vdw 2.239 3.120 nonbonded pdb=" OD1 ASN B 6 " pdb=" OG1 THR B 48 " model vdw 2.243 3.040 nonbonded pdb=" OD1 ASP A 486 " pdb="MG MG A1003 " model vdw 2.245 2.170 ... (remaining 64356 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.860 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 8350 Z= 0.203 Angle : 0.592 11.289 11343 Z= 0.292 Chirality : 0.040 0.158 1342 Planarity : 0.003 0.034 1431 Dihedral : 12.069 124.661 2946 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.43 % Favored : 96.47 % Rotamer: Outliers : 0.12 % Allowed : 4.72 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.24), residues: 1049 helix: -0.18 (0.21), residues: 476 sheet: -2.02 (0.35), residues: 189 loop : -2.55 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 88 TYR 0.011 0.001 TYR B 2 PHE 0.012 0.001 PHE A 607 TRP 0.003 0.001 TRP B 22 HIS 0.002 0.001 HIS A 539 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.20 ( 8350) covalent geometry : angle 0.59189 / 0.29 (11343) hydrogen bonds : bond 0.15541 / 10.31 ( 441) hydrogen bonds : angle 6.11334 / 4.25 ( 1260) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8286 (pp20) cc_final: 0.7546 (pp20) REVERT: A 255 TYR cc_start: 0.7250 (m-80) cc_final: 0.6734 (m-10) REVERT: A 399 TYR cc_start: 0.8432 (m-80) cc_final: 0.7619 (m-10) REVERT: A 443 LEU cc_start: 0.8824 (tp) cc_final: 0.8605 (tp) REVERT: A 444 GLU cc_start: 0.8808 (tp30) cc_final: 0.8363 (tm-30) REVERT: A 452 ASP cc_start: 0.8567 (t0) cc_final: 0.8353 (t0) REVERT: A 583 PHE cc_start: 0.8735 (m-80) cc_final: 0.8223 (m-80) REVERT: A 591 MET cc_start: 0.8850 (tpp) cc_final: 0.8368 (tpt) REVERT: A 597 PHE cc_start: 0.8246 (m-80) cc_final: 0.8021 (m-80) REVERT: B 73 MET cc_start: 0.8435 (tpp) cc_final: 0.8040 (tpt) REVERT: B 284 LEU cc_start: 0.9155 (mt) cc_final: 0.8890 (mp) REVERT: B 479 TYR cc_start: 0.8549 (t80) cc_final: 0.8179 (t80) REVERT: B 480 MET cc_start: 0.8763 (ttt) cc_final: 0.8563 (ttt) REVERT: B 563 ASN cc_start: 0.7915 (p0) cc_final: 0.7706 (p0) REVERT: B 569 TYR cc_start: 0.8868 (t80) cc_final: 0.8572 (t80) outliers start: 1 outliers final: 0 residues processed: 145 average time/residue: 0.0807 time to fit residues: 16.7069 Evaluate side-chains 97 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.0870 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.0970 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS A 303 ASN A 422 GLN B 242 GLN B 266 HIS B 408 HIS B 437 HIS B 451 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.084582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.069235 restraints weight = 28897.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.071766 restraints weight = 14209.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.073422 restraints weight = 8769.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.074567 restraints weight = 6289.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.075319 restraints weight = 4964.299| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8350 Z= 0.117 Angle : 0.564 8.734 11343 Z= 0.286 Chirality : 0.042 0.142 1342 Planarity : 0.004 0.040 1431 Dihedral : 7.877 134.981 1160 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.94 % Allowed : 12.51 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.26), residues: 1049 helix: 0.78 (0.23), residues: 486 sheet: -1.70 (0.36), residues: 186 loop : -2.08 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 139 TYR 0.009 0.001 TYR B 479 PHE 0.020 0.001 PHE A 458 TRP 0.038 0.005 TRP B 602 HIS 0.011 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 8350) covalent geometry : angle 0.56382 / 0.29 (11343) hydrogen bonds : bond 0.04057 / 2.86 ( 441) hydrogen bonds : angle 4.73908 / 3.29 ( 1260) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8339 (pp20) cc_final: 0.7679 (pp20) REVERT: A 255 TYR cc_start: 0.7364 (m-80) cc_final: 0.7126 (m-10) REVERT: A 399 TYR cc_start: 0.8450 (m-80) cc_final: 0.7801 (m-10) REVERT: A 423 ASP cc_start: 0.8947 (t70) cc_final: 0.8479 (t0) REVERT: A 444 GLU cc_start: 0.8532 (tp30) cc_final: 0.8250 (tm-30) REVERT: A 591 MET cc_start: 0.8775 (tpp) cc_final: 0.8283 (tpt) REVERT: B 106 ASP cc_start: 0.8785 (t0) cc_final: 0.8134 (t0) REVERT: B 284 LEU cc_start: 0.8934 (mt) cc_final: 0.8598 (mp) REVERT: B 338 LEU cc_start: 0.9173 (mt) cc_final: 0.8933 (tp) REVERT: B 564 VAL cc_start: 0.9295 (t) cc_final: 0.8976 (p) REVERT: B 569 TYR cc_start: 0.8598 (t80) cc_final: 0.8163 (t80) outliers start: 8 outliers final: 5 residues processed: 115 average time/residue: 0.0560 time to fit residues: 10.4000 Evaluate side-chains 109 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain B residue 303 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 69 optimal weight: 0.3980 chunk 92 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 419 ASN ** 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 = 0.3309 r_free = 0.3309 target = 0.083981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.068027 restraints weight = 33212.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.070689 restraints weight = 15699.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.072477 restraints weight = 9468.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.073678 restraints weight = 6662.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.074462 restraints weight = 5209.210| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8350 Z= 0.127 Angle : 0.562 8.483 11343 Z= 0.282 Chirality : 0.042 0.187 1342 Planarity : 0.004 0.042 1431 Dihedral : 7.981 141.602 1160 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.36 % Allowed : 14.05 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.26), residues: 1049 helix: 1.03 (0.23), residues: 487 sheet: -1.37 (0.38), residues: 185 loop : -1.90 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 139 TYR 0.009 0.001 TYR B 136 PHE 0.020 0.001 PHE B 433 TRP 0.022 0.003 TRP B 602 HIS 0.003 0.001 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 8350) covalent geometry : angle 0.56210 / 0.28 (11343) hydrogen bonds : bond 0.04003 / 2.84 ( 441) hydrogen bonds : angle 4.48419 / 3.11 ( 1260) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8379 (pp20) cc_final: 0.7726 (pp20) REVERT: A 151 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8681 (mp) REVERT: A 399 TYR cc_start: 0.8465 (m-80) cc_final: 0.7806 (m-10) REVERT: A 423 ASP cc_start: 0.8965 (t70) cc_final: 0.8709 (t0) REVERT: A 591 MET cc_start: 0.8699 (tpp) cc_final: 0.8252 (tpt) REVERT: B 164 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8020 (mtm) REVERT: B 284 LEU cc_start: 0.8958 (mt) cc_final: 0.8674 (mp) outliers start: 20 outliers final: 13 residues processed: 115 average time/residue: 0.0609 time to fit residues: 11.2213 Evaluate side-chains 111 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 474 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 92 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 419 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.083422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.066725 restraints weight = 43472.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.069621 restraints weight = 18104.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.071540 restraints weight = 10273.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.072854 restraints weight = 6989.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.073769 restraints weight = 5325.680| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8350 Z= 0.115 Angle : 0.553 9.006 11343 Z= 0.278 Chirality : 0.042 0.136 1342 Planarity : 0.004 0.041 1431 Dihedral : 8.096 143.322 1160 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.60 % Allowed : 14.99 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.26), residues: 1049 helix: 1.18 (0.23), residues: 487 sheet: -1.21 (0.38), residues: 186 loop : -1.74 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 381 TYR 0.037 0.001 TYR B 569 PHE 0.033 0.001 PHE A 458 TRP 0.052 0.005 TRP B 602 HIS 0.003 0.001 HIS B 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 8350) covalent geometry : angle 0.55272 / 0.28 (11343) hydrogen bonds : bond 0.03894 / 2.75 ( 441) hydrogen bonds : angle 4.39929 / 3.06 ( 1260) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8393 (pp20) cc_final: 0.7764 (pp20) REVERT: A 151 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8689 (mp) REVERT: A 399 TYR cc_start: 0.8456 (m-80) cc_final: 0.7825 (m-10) REVERT: A 423 ASP cc_start: 0.8969 (t70) cc_final: 0.8712 (t0) REVERT: A 591 MET cc_start: 0.8721 (tpp) cc_final: 0.8283 (tpt) REVERT: B 164 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7924 (mtm) REVERT: B 284 LEU cc_start: 0.8961 (mt) cc_final: 0.8656 (mp) REVERT: B 569 TYR cc_start: 0.8617 (t80) cc_final: 0.7749 (t80) outliers start: 22 outliers final: 13 residues processed: 113 average time/residue: 0.0576 time to fit residues: 10.6191 Evaluate side-chains 111 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 474 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 37 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.081281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.064181 restraints weight = 43980.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.067044 restraints weight = 18688.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.068984 restraints weight = 10746.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.070237 restraints weight = 7336.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.071160 restraints weight = 5691.457| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8350 Z= 0.188 Angle : 0.578 6.897 11343 Z= 0.295 Chirality : 0.043 0.137 1342 Planarity : 0.004 0.041 1431 Dihedral : 8.308 141.910 1160 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.95 % Allowed : 15.11 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.26), residues: 1049 helix: 1.27 (0.23), residues: 487 sheet: -1.10 (0.38), residues: 184 loop : -1.67 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 381 TYR 0.033 0.001 TYR B 569 PHE 0.033 0.002 PHE A 458 TRP 0.031 0.004 TRP B 602 HIS 0.004 0.001 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 ( 8350) covalent geometry : angle 0.57842 / 0.29 (11343) hydrogen bonds : bond 0.04080 / 2.88 ( 441) hydrogen bonds : angle 4.35587 / 3.02 ( 1260) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8401 (pp20) cc_final: 0.7739 (pp20) REVERT: A 148 ASP cc_start: 0.7780 (p0) cc_final: 0.7548 (p0) REVERT: A 151 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8668 (mp) REVERT: A 296 MET cc_start: 0.8394 (mmt) cc_final: 0.8018 (mmp) REVERT: A 339 MET cc_start: 0.8663 (mmp) cc_final: 0.8432 (mmm) REVERT: A 399 TYR cc_start: 0.8503 (m-80) cc_final: 0.8278 (m-10) REVERT: A 423 ASP cc_start: 0.9008 (t70) cc_final: 0.8759 (t0) REVERT: A 591 MET cc_start: 0.8728 (tpp) cc_final: 0.8277 (tpt) REVERT: B 164 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7897 (mtm) REVERT: B 284 LEU cc_start: 0.9050 (mt) cc_final: 0.8820 (mp) outliers start: 25 outliers final: 16 residues processed: 105 average time/residue: 0.0639 time to fit residues: 10.7199 Evaluate side-chains 106 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 474 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 26 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 102 optimal weight: 0.3980 chunk 63 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.083183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.067287 restraints weight = 32807.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.069889 restraints weight = 15375.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.071649 restraints weight = 9258.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.072810 restraints weight = 6538.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.073529 restraints weight = 5137.167| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8350 Z= 0.116 Angle : 0.565 10.171 11343 Z= 0.281 Chirality : 0.042 0.153 1342 Planarity : 0.003 0.040 1431 Dihedral : 8.311 141.758 1160 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.60 % Allowed : 16.17 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.26), residues: 1049 helix: 1.29 (0.23), residues: 488 sheet: -0.94 (0.38), residues: 184 loop : -1.57 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 360 TYR 0.017 0.001 TYR B 479 PHE 0.033 0.001 PHE A 458 TRP 0.027 0.004 TRP B 602 HIS 0.003 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 8350) covalent geometry : angle 0.56535 / 0.28 (11343) hydrogen bonds : bond 0.03894 / 2.75 ( 441) hydrogen bonds : angle 4.25646 / 2.98 ( 1260) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8463 (pp20) cc_final: 0.7821 (pp20) REVERT: A 296 MET cc_start: 0.8357 (mmt) cc_final: 0.7994 (mmp) REVERT: A 339 MET cc_start: 0.8626 (mmp) cc_final: 0.8372 (mmm) REVERT: A 399 TYR cc_start: 0.8464 (m-80) cc_final: 0.8241 (m-10) REVERT: A 423 ASP cc_start: 0.8969 (t70) cc_final: 0.8705 (t0) REVERT: A 591 MET cc_start: 0.8687 (tpp) cc_final: 0.8252 (tpt) REVERT: B 164 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7929 (mtm) REVERT: B 284 LEU cc_start: 0.8972 (mt) cc_final: 0.8696 (mp) outliers start: 22 outliers final: 13 residues processed: 115 average time/residue: 0.0595 time to fit residues: 11.0649 Evaluate side-chains 102 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 474 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 101 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.081789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.066059 restraints weight = 28503.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.068506 restraints weight = 14205.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.070139 restraints weight = 8878.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.071238 restraints weight = 6426.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.071836 restraints weight = 5135.962| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8350 Z= 0.167 Angle : 0.594 11.217 11343 Z= 0.297 Chirality : 0.042 0.146 1342 Planarity : 0.004 0.040 1431 Dihedral : 8.446 141.338 1160 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.24 % Allowed : 17.71 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.26), residues: 1049 helix: 1.32 (0.24), residues: 489 sheet: -0.92 (0.38), residues: 184 loop : -1.52 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 381 TYR 0.018 0.001 TYR B 569 PHE 0.038 0.002 PHE B 433 TRP 0.026 0.004 TRP B 602 HIS 0.003 0.001 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 8350) covalent geometry : angle 0.59400 / 0.30 (11343) hydrogen bonds : bond 0.04007 / 2.80 ( 441) hydrogen bonds : angle 4.29636 / 3.02 ( 1260) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8458 (pp20) cc_final: 0.7818 (pp20) REVERT: A 296 MET cc_start: 0.8447 (mmt) cc_final: 0.8118 (mmp) REVERT: A 339 MET cc_start: 0.8714 (mmp) cc_final: 0.8464 (mmm) REVERT: A 399 TYR cc_start: 0.8491 (m-80) cc_final: 0.8246 (m-10) REVERT: A 423 ASP cc_start: 0.8998 (t70) cc_final: 0.8558 (t0) REVERT: A 591 MET cc_start: 0.8731 (tpp) cc_final: 0.8293 (tpt) REVERT: B 164 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.8060 (mtm) REVERT: B 284 LEU cc_start: 0.9047 (mt) cc_final: 0.8812 (mp) outliers start: 19 outliers final: 14 residues processed: 102 average time/residue: 0.0579 time to fit residues: 9.6642 Evaluate side-chains 104 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 474 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 33 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 chunk 74 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 47 optimal weight: 0.0670 chunk 53 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.083577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.068569 restraints weight = 23606.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.070847 restraints weight = 12330.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.072393 restraints weight = 7924.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.073442 restraints weight = 5832.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.074134 restraints weight = 4702.087| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8350 Z= 0.117 Angle : 0.598 13.155 11343 Z= 0.293 Chirality : 0.042 0.157 1342 Planarity : 0.004 0.040 1431 Dihedral : 8.391 140.850 1160 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.24 % Allowed : 17.83 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.26), residues: 1049 helix: 1.33 (0.24), residues: 488 sheet: -0.78 (0.39), residues: 184 loop : -1.52 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 552 TYR 0.018 0.001 TYR B 479 PHE 0.031 0.001 PHE A 458 TRP 0.023 0.003 TRP B 602 HIS 0.003 0.001 HIS A 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 8350) covalent geometry : angle 0.59834 / 0.29 (11343) hydrogen bonds : bond 0.03850 / 2.71 ( 441) hydrogen bonds : angle 4.23665 / 2.98 ( 1260) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8458 (pp20) cc_final: 0.7819 (pp20) REVERT: A 205 PHE cc_start: 0.6254 (m-80) cc_final: 0.6046 (m-80) REVERT: A 296 MET cc_start: 0.8303 (mmt) cc_final: 0.7967 (mmp) REVERT: A 339 MET cc_start: 0.8729 (mmp) cc_final: 0.8471 (mmm) REVERT: A 399 TYR cc_start: 0.8454 (m-80) cc_final: 0.8215 (m-10) REVERT: A 423 ASP cc_start: 0.8982 (t70) cc_final: 0.8727 (t0) REVERT: A 591 MET cc_start: 0.8695 (tpp) cc_final: 0.8269 (tpt) REVERT: B 69 MET cc_start: 0.8545 (ptp) cc_final: 0.7971 (ppp) REVERT: B 106 ASP cc_start: 0.8813 (t0) cc_final: 0.8227 (t0) REVERT: B 164 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7991 (mtm) REVERT: B 284 LEU cc_start: 0.8977 (mt) cc_final: 0.8717 (mp) outliers start: 19 outliers final: 14 residues processed: 105 average time/residue: 0.0486 time to fit residues: 8.2888 Evaluate side-chains 104 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 474 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 22 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 74 optimal weight: 0.0570 chunk 86 optimal weight: 0.1980 chunk 50 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 105 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.083970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.068321 restraints weight = 28338.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.070829 restraints weight = 13951.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.072501 restraints weight = 8647.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.073647 restraints weight = 6216.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.074348 restraints weight = 4933.996| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8350 Z= 0.117 Angle : 0.593 12.852 11343 Z= 0.293 Chirality : 0.042 0.161 1342 Planarity : 0.004 0.040 1431 Dihedral : 8.477 147.299 1160 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.01 % Allowed : 18.54 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.26), residues: 1049 helix: 1.38 (0.24), residues: 487 sheet: -0.69 (0.39), residues: 184 loop : -1.46 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 574 TYR 0.010 0.001 TYR A 510 PHE 0.030 0.001 PHE A 458 TRP 0.023 0.003 TRP B 602 HIS 0.003 0.001 HIS B 524 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 8350) covalent geometry : angle 0.59307 / 0.29 (11343) hydrogen bonds : bond 0.03804 / 2.68 ( 441) hydrogen bonds : angle 4.21403 / 2.97 ( 1260) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8437 (pp20) cc_final: 0.7808 (pp20) REVERT: A 205 PHE cc_start: 0.6300 (m-80) cc_final: 0.6097 (m-80) REVERT: A 296 MET cc_start: 0.8311 (mmt) cc_final: 0.7979 (mmp) REVERT: A 339 MET cc_start: 0.8744 (mmp) cc_final: 0.8537 (mmm) REVERT: A 399 TYR cc_start: 0.8459 (m-80) cc_final: 0.8234 (m-10) REVERT: A 423 ASP cc_start: 0.8969 (t70) cc_final: 0.8522 (t0) REVERT: A 591 MET cc_start: 0.8673 (tpp) cc_final: 0.8260 (tpt) REVERT: B 164 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7989 (mtm) REVERT: B 284 LEU cc_start: 0.8982 (mt) cc_final: 0.8718 (mp) REVERT: B 569 TYR cc_start: 0.8637 (t80) cc_final: 0.8403 (t80) outliers start: 17 outliers final: 15 residues processed: 108 average time/residue: 0.0525 time to fit residues: 9.1516 Evaluate side-chains 110 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 474 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 35 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 406 HIS ** B 586 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 = 0.3296 r_free = 0.3296 target = 0.082697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.066047 restraints weight = 43367.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.068918 restraints weight = 18469.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.070837 restraints weight = 10603.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.072149 restraints weight = 7277.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.072984 restraints weight = 5576.476| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8350 Z= 0.147 Angle : 0.618 12.981 11343 Z= 0.304 Chirality : 0.042 0.151 1342 Planarity : 0.004 0.040 1431 Dihedral : 8.409 141.554 1160 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.77 % Allowed : 18.77 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.27), residues: 1049 helix: 1.40 (0.24), residues: 487 sheet: -0.69 (0.39), residues: 184 loop : -1.41 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 238 TYR 0.016 0.001 TYR B 479 PHE 0.044 0.002 PHE A 458 TRP 0.020 0.003 TRP B 602 HIS 0.009 0.001 HIS B 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 8350) covalent geometry : angle 0.61780 / 0.30 (11343) hydrogen bonds : bond 0.03898 / 2.74 ( 441) hydrogen bonds : angle 4.24843 / 2.99 ( 1260) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8443 (pp20) cc_final: 0.7806 (pp20) REVERT: A 296 MET cc_start: 0.8294 (mmt) cc_final: 0.7967 (mmp) REVERT: A 339 MET cc_start: 0.8732 (mmp) cc_final: 0.8493 (mmm) REVERT: A 399 TYR cc_start: 0.8465 (m-80) cc_final: 0.8235 (m-10) REVERT: A 423 ASP cc_start: 0.8968 (t70) cc_final: 0.8525 (t0) REVERT: A 516 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7996 (mp10) REVERT: A 591 MET cc_start: 0.8677 (tpp) cc_final: 0.8267 (tpt) REVERT: B 284 LEU cc_start: 0.8999 (mt) cc_final: 0.8740 (mp) REVERT: B 569 TYR cc_start: 0.8513 (t80) cc_final: 0.8268 (t80) outliers start: 15 outliers final: 13 residues processed: 107 average time/residue: 0.0464 time to fit residues: 8.0406 Evaluate side-chains 107 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 474 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 0.0870 chunk 105 optimal weight: 0.1980 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 271 HIS B 586 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.083969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.068261 restraints weight = 34024.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.070888 restraints weight = 15797.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.072659 restraints weight = 9432.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.073862 restraints weight = 6632.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.074580 restraints weight = 5177.248| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8350 Z= 0.115 Angle : 0.597 12.600 11343 Z= 0.295 Chirality : 0.042 0.158 1342 Planarity : 0.003 0.040 1431 Dihedral : 8.328 140.809 1160 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.77 % Allowed : 18.89 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.27), residues: 1049 helix: 1.36 (0.24), residues: 488 sheet: -0.55 (0.40), residues: 183 loop : -1.37 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 552 TYR 0.013 0.001 TYR B 49 PHE 0.043 0.001 PHE A 458 TRP 0.022 0.003 TRP B 602 HIS 0.006 0.001 HIS B 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 8350) covalent geometry : angle 0.59709 / 0.29 (11343) hydrogen bonds : bond 0.03862 / 2.72 ( 441) hydrogen bonds : angle 4.22726 / 2.97 ( 1260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1498.84 seconds wall clock time: 26 minutes 42.32 seconds (1602.32 seconds total)