Starting phenix.real_space_refine on Fri Nov 15 06:27:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yfw_39231/11_2024/8yfw_39231.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yfw_39231/11_2024/8yfw_39231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yfw_39231/11_2024/8yfw_39231.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yfw_39231/11_2024/8yfw_39231.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yfw_39231/11_2024/8yfw_39231.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yfw_39231/11_2024/8yfw_39231.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 5511 2.51 5 N 1423 2.21 5 O 1453 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8419 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4222 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 168} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 562} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 647 Unresolved non-hydrogen angles: 817 Unresolved non-hydrogen dihedrals: 541 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 4, 'TYR:plan': 7, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 12, 'GLU:plan': 20, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 391 Chain: "B" Number of atoms: 4197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4197 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 164} Link IDs: {'PTRANS': 19, 'TRANS': 558} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 624 Unresolved non-hydrogen angles: 787 Unresolved non-hydrogen dihedrals: 520 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 11, 'GLU:plan': 19, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 370 Time building chain proxies: 5.53, per 1000 atoms: 0.66 Number of scatterers: 8419 At special positions: 0 Unit cell: (121, 127.6, 127.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1453 8.00 N 1423 7.00 C 5511 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 440 " distance=2.03 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 440 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.2 seconds 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2230 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 78.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 21 through 36 Processing helix chain 'A' and resid 43 through 100 Processing helix chain 'A' and resid 119 through 168 Processing helix chain 'A' and resid 170 through 180 removed outlier: 3.533A pdb=" N ASP A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 188 Processing helix chain 'A' and resid 189 through 206 removed outlier: 3.847A pdb=" N GLN A 193 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'A' and resid 230 through 258 removed outlier: 3.910A pdb=" N THR A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 295 removed outlier: 3.551A pdb=" N ILE A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 337 removed outlier: 3.548A pdb=" N LEU A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 390 through 402 removed outlier: 3.748A pdb=" N PHE A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 419 removed outlier: 4.058A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A 419 " --> pdb=" O CYS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 471 removed outlier: 4.311A pdb=" N ILE A 450 " --> pdb=" O GLY A 446 " (cutoff:3.500A) Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 476 through 500 removed outlier: 4.253A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 532 removed outlier: 4.069A pdb=" N PHE A 510 " --> pdb=" O ASP A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 570 removed outlier: 4.081A pdb=" N TYR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 581 removed outlier: 3.970A pdb=" N ILE A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 579 " --> pdb=" O ILE A 575 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 597 removed outlier: 3.944A pdb=" N ILE A 592 " --> pdb=" O SER A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 616 removed outlier: 3.798A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU A 612 " --> pdb=" O ASN A 608 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU A 613 " --> pdb=" O PHE A 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 36 removed outlier: 3.583A pdb=" N GLN B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 100 removed outlier: 3.804A pdb=" N VAL B 47 " --> pdb=" O ASP B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 168 Processing helix chain 'B' and resid 170 through 179 Processing helix chain 'B' and resid 183 through 188 removed outlier: 3.795A pdb=" N THR B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 206 removed outlier: 3.888A pdb=" N GLN B 193 " --> pdb=" O LYS B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 Processing helix chain 'B' and resid 230 through 258 removed outlier: 3.559A pdb=" N THR B 234 " --> pdb=" O PRO B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 296 removed outlier: 4.373A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 removed outlier: 3.552A pdb=" N ILE B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 337 Processing helix chain 'B' and resid 346 through 360 removed outlier: 3.609A pdb=" N ALA B 350 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 351 " --> pdb=" O TYR B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 384 removed outlier: 3.630A pdb=" N PHE B 372 " --> pdb=" O TYR B 368 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B 383 " --> pdb=" O PHE B 379 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA B 384 " --> pdb=" O ARG B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 403 removed outlier: 3.597A pdb=" N SER B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 420 removed outlier: 3.801A pdb=" N MET B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LEU B 410 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU B 411 " --> pdb=" O LEU B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 471 removed outlier: 4.511A pdb=" N ALA B 449 " --> pdb=" O TYR B 445 " (cutoff:3.500A) Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 473 through 501 removed outlier: 4.306A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU B 501 " --> pdb=" O SER B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 532 removed outlier: 4.413A pdb=" N TYR B 512 " --> pdb=" O MET B 508 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE B 515 " --> pdb=" O PHE B 511 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL B 516 " --> pdb=" O TYR B 512 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE B 519 " --> pdb=" O ILE B 515 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER B 521 " --> pdb=" O PHE B 517 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TYR B 524 " --> pdb=" O ILE B 520 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET B 532 " --> pdb=" O TRP B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 571 removed outlier: 4.035A pdb=" N TYR B 559 " --> pdb=" O GLN B 555 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 580 removed outlier: 3.967A pdb=" N GLN B 576 " --> pdb=" O ALA B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 620 Proline residue: B 598 - end of helix removed outlier: 3.811A pdb=" N VAL B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 606 " --> pdb=" O PHE B 602 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 612 " --> pdb=" O ASN B 608 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU B 613 " --> pdb=" O PHE B 609 " (cutoff:3.500A) 667 hydrogen bonds defined for protein. 2001 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: 2.30 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2684 1.34 - 1.46: 2048 1.46 - 1.58: 3861 1.58 - 1.70: 0 1.70 - 1.81: 44 Bond restraints: 8637 Sorted by residual: bond pdb=" CB CYS B 415 " pdb=" SG CYS B 415 " ideal model delta sigma weight residual 1.808 1.733 0.075 3.30e-02 9.18e+02 5.19e+00 bond pdb=" CB CYS B 440 " pdb=" SG CYS B 440 " ideal model delta sigma weight residual 1.808 1.743 0.065 3.30e-02 9.18e+02 3.93e+00 bond pdb=" CB PRO B 307 " pdb=" CG PRO B 307 " ideal model delta sigma weight residual 1.492 1.577 -0.085 5.00e-02 4.00e+02 2.87e+00 bond pdb=" CB PRO B 343 " pdb=" CG PRO B 343 " ideal model delta sigma weight residual 1.492 1.561 -0.069 5.00e-02 4.00e+02 1.93e+00 bond pdb=" CB PRO B 586 " pdb=" CG PRO B 586 " ideal model delta sigma weight residual 1.492 1.557 -0.065 5.00e-02 4.00e+02 1.67e+00 ... (remaining 8632 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.99: 11762 3.99 - 7.97: 57 7.97 - 11.96: 3 11.96 - 15.94: 0 15.94 - 19.93: 1 Bond angle restraints: 11823 Sorted by residual: angle pdb=" C ALA A 226 " pdb=" N GLN A 227 " pdb=" CA GLN A 227 " ideal model delta sigma weight residual 121.70 141.63 -19.93 1.80e+00 3.09e-01 1.23e+02 angle pdb=" C SER B 340 " pdb=" CA SER B 340 " pdb=" CB SER B 340 " ideal model delta sigma weight residual 116.54 110.08 6.46 1.15e+00 7.56e-01 3.16e+01 angle pdb=" CA PRO B 307 " pdb=" N PRO B 307 " pdb=" CD PRO B 307 " ideal model delta sigma weight residual 112.00 104.68 7.32 1.40e+00 5.10e-01 2.74e+01 angle pdb=" C ILE A 454 " pdb=" CA ILE A 454 " pdb=" CB ILE A 454 " ideal model delta sigma weight residual 113.70 109.08 4.62 9.50e-01 1.11e+00 2.37e+01 angle pdb=" C THR B 383 " pdb=" N ALA B 384 " pdb=" CA ALA B 384 " ideal model delta sigma weight residual 121.80 131.66 -9.86 2.44e+00 1.68e-01 1.63e+01 ... (remaining 11818 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 4365 17.52 - 35.04: 455 35.04 - 52.56: 112 52.56 - 70.07: 15 70.07 - 87.59: 8 Dihedral angle restraints: 4955 sinusoidal: 1526 harmonic: 3429 Sorted by residual: dihedral pdb=" CB CYS B 415 " pdb=" SG CYS B 415 " pdb=" SG CYS B 440 " pdb=" CB CYS B 440 " ideal model delta sinusoidal sigma weight residual 93.00 178.72 -85.72 1 1.00e+01 1.00e-02 8.88e+01 dihedral pdb=" CB CYS A 415 " pdb=" SG CYS A 415 " pdb=" SG CYS A 440 " pdb=" CB CYS A 440 " ideal model delta sinusoidal sigma weight residual 93.00 159.03 -66.03 1 1.00e+01 1.00e-02 5.70e+01 dihedral pdb=" CA CYS A 440 " pdb=" C CYS A 440 " pdb=" N HIS A 441 " pdb=" CA HIS A 441 " ideal model delta harmonic sigma weight residual 180.00 152.36 27.64 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 4952 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1152 0.053 - 0.107: 195 0.107 - 0.160: 24 0.160 - 0.213: 3 0.213 - 0.266: 1 Chirality restraints: 1375 Sorted by residual: chirality pdb=" CB ILE B 271 " pdb=" CA ILE B 271 " pdb=" CG1 ILE B 271 " pdb=" CG2 ILE B 271 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA CYS A 440 " pdb=" N CYS A 440 " pdb=" C CYS A 440 " pdb=" CB CYS A 440 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.80e-01 chirality pdb=" CG LEU B 284 " pdb=" CB LEU B 284 " pdb=" CD1 LEU B 284 " pdb=" CD2 LEU B 284 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.67e-01 ... (remaining 1372 not shown) Planarity restraints: 1499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 306 " -0.113 5.00e-02 4.00e+02 1.68e-01 4.51e+01 pdb=" N PRO B 307 " 0.290 5.00e-02 4.00e+02 pdb=" CA PRO B 307 " -0.094 5.00e-02 4.00e+02 pdb=" CD PRO B 307 " -0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 585 " -0.046 5.00e-02 4.00e+02 6.84e-02 7.50e+00 pdb=" N PRO B 586 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 586 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 586 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 361 " -0.042 5.00e-02 4.00e+02 6.37e-02 6.49e+00 pdb=" N PRO B 362 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 362 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 362 " -0.035 5.00e-02 4.00e+02 ... (remaining 1496 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 214 2.70 - 3.25: 9026 3.25 - 3.80: 13801 3.80 - 4.35: 15198 4.35 - 4.90: 25311 Nonbonded interactions: 63550 Sorted by model distance: nonbonded pdb=" O ILE A 575 " pdb=" OG SER A 578 " model vdw 2.152 3.040 nonbonded pdb=" ND2 ASN B 288 " pdb=" OD1 ASN B 608 " model vdw 2.156 3.120 nonbonded pdb=" OE1 GLU B 318 " pdb=" OH TYR B 367 " model vdw 2.182 3.040 nonbonded pdb=" OG SER B 340 " pdb=" N VAL B 341 " model vdw 2.183 3.120 nonbonded pdb=" OD1 ASN B 618 " pdb=" N ASN B 619 " model vdw 2.189 3.120 ... (remaining 63545 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 26 through 620) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.590 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 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 0.085 8637 Z= 0.222 Angle : 0.737 19.928 11823 Z= 0.409 Chirality : 0.041 0.266 1375 Planarity : 0.006 0.168 1499 Dihedral : 15.862 87.593 2719 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.68 % Favored : 94.97 % Rotamer: Outliers : 0.28 % Allowed : 30.77 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.26), residues: 1153 helix: 2.18 (0.18), residues: 854 sheet: None (None), residues: 0 loop : -2.16 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 373 HIS 0.005 0.001 HIS A 299 PHE 0.028 0.002 PHE B 357 TYR 0.033 0.002 TYR B 412 ARG 0.007 0.001 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 147 time to evaluate : 0.945 Fit side-chains REVERT: B 506 ASP cc_start: 0.6490 (t0) cc_final: 0.6279 (t0) outliers start: 2 outliers final: 2 residues processed: 148 average time/residue: 0.1599 time to fit residues: 35.3287 Evaluate side-chains 145 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 143 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 416 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 2.9990 chunk 87 optimal weight: 0.0020 chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 50.0000 chunk 46 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 0.0010 chunk 67 optimal weight: 30.0000 chunk 104 optimal weight: 5.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 576 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.0870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8637 Z= 0.186 Angle : 0.596 9.785 11823 Z= 0.320 Chirality : 0.038 0.157 1375 Planarity : 0.005 0.124 1499 Dihedral : 4.062 26.961 1242 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.99 % Favored : 95.75 % Rotamer: Outliers : 3.56 % Allowed : 23.08 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.25), residues: 1153 helix: 2.50 (0.17), residues: 869 sheet: None (None), residues: 0 loop : -2.07 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 373 HIS 0.004 0.001 HIS A 299 PHE 0.025 0.001 PHE B 335 TYR 0.026 0.001 TYR B 412 ARG 0.005 0.001 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: A 290 TYR cc_start: 0.7209 (t80) cc_final: 0.6828 (t80) outliers start: 25 outliers final: 11 residues processed: 169 average time/residue: 0.1621 time to fit residues: 39.9592 Evaluate side-chains 151 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 499 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 50.0000 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 71 optimal weight: 0.0570 chunk 28 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 113 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8637 Z= 0.180 Angle : 0.581 10.056 11823 Z= 0.309 Chirality : 0.039 0.145 1375 Planarity : 0.004 0.094 1499 Dihedral : 3.856 23.838 1239 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.08 % Favored : 95.66 % Rotamer: Outliers : 3.85 % Allowed : 21.37 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.25), residues: 1153 helix: 2.65 (0.17), residues: 877 sheet: None (None), residues: 0 loop : -2.07 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 373 HIS 0.004 0.001 HIS A 299 PHE 0.022 0.001 PHE B 335 TYR 0.037 0.001 TYR B 412 ARG 0.003 0.000 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 290 TYR cc_start: 0.6819 (t80) cc_final: 0.6207 (t80) outliers start: 27 outliers final: 18 residues processed: 167 average time/residue: 0.1660 time to fit residues: 40.7680 Evaluate side-chains 152 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 616 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 50.0000 chunk 49 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8637 Z= 0.195 Angle : 0.570 10.061 11823 Z= 0.305 Chirality : 0.038 0.141 1375 Planarity : 0.004 0.085 1499 Dihedral : 3.808 21.913 1239 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.16 % Favored : 95.58 % Rotamer: Outliers : 4.42 % Allowed : 23.08 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.25), residues: 1153 helix: 2.75 (0.17), residues: 870 sheet: None (None), residues: 0 loop : -2.03 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 528 HIS 0.004 0.001 HIS B 313 PHE 0.020 0.001 PHE A 511 TYR 0.034 0.001 TYR B 412 ARG 0.003 0.000 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.998 Fit side-chains REVERT: A 290 TYR cc_start: 0.6892 (t80) cc_final: 0.6421 (t80) REVERT: A 294 GLN cc_start: 0.5337 (OUTLIER) cc_final: 0.5006 (tm-30) REVERT: B 244 PHE cc_start: 0.8079 (t80) cc_final: 0.7463 (t80) REVERT: B 347 TYR cc_start: 0.6183 (m-80) cc_final: 0.5856 (m-80) REVERT: B 364 LYS cc_start: 0.7487 (tttt) cc_final: 0.7103 (mmpt) outliers start: 31 outliers final: 20 residues processed: 168 average time/residue: 0.1721 time to fit residues: 43.2638 Evaluate side-chains 155 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 576 GLN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 616 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 56 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8637 Z= 0.207 Angle : 0.586 10.039 11823 Z= 0.314 Chirality : 0.039 0.142 1375 Planarity : 0.004 0.079 1499 Dihedral : 3.747 18.946 1239 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.64 % Favored : 96.10 % Rotamer: Outliers : 3.85 % Allowed : 23.65 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.25), residues: 1153 helix: 2.78 (0.17), residues: 871 sheet: None (None), residues: 0 loop : -2.02 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 292 HIS 0.003 0.001 HIS B 313 PHE 0.022 0.001 PHE B 487 TYR 0.045 0.002 TYR B 412 ARG 0.003 0.000 ARG B 308 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: B 244 PHE cc_start: 0.8126 (t80) cc_final: 0.7431 (t80) REVERT: B 364 LYS cc_start: 0.7479 (tttt) cc_final: 0.7169 (mmpt) REVERT: B 409 ASP cc_start: 0.6461 (p0) cc_final: 0.6255 (p0) outliers start: 27 outliers final: 22 residues processed: 161 average time/residue: 0.1756 time to fit residues: 40.6489 Evaluate side-chains 164 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 616 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 40.0000 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 50.0000 chunk 107 optimal weight: 0.4980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8637 Z= 0.235 Angle : 0.590 10.021 11823 Z= 0.316 Chirality : 0.039 0.157 1375 Planarity : 0.004 0.074 1499 Dihedral : 3.822 19.360 1239 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.34 % Favored : 95.40 % Rotamer: Outliers : 4.84 % Allowed : 23.65 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.25), residues: 1153 helix: 2.71 (0.17), residues: 871 sheet: None (None), residues: 0 loop : -2.02 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 266 HIS 0.005 0.001 HIS B 313 PHE 0.026 0.002 PHE A 511 TYR 0.033 0.002 TYR B 412 ARG 0.005 0.000 ARG B 448 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: B 244 PHE cc_start: 0.8228 (t80) cc_final: 0.7409 (t80) REVERT: B 266 TRP cc_start: 0.8309 (m100) cc_final: 0.8094 (m100) REVERT: B 364 LYS cc_start: 0.7670 (tttt) cc_final: 0.7305 (mmpt) outliers start: 34 outliers final: 26 residues processed: 164 average time/residue: 0.1693 time to fit residues: 40.7225 Evaluate side-chains 159 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 616 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 69 optimal weight: 50.0000 chunk 67 optimal weight: 40.0000 chunk 51 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8637 Z= 0.249 Angle : 0.608 9.869 11823 Z= 0.323 Chirality : 0.039 0.172 1375 Planarity : 0.004 0.073 1499 Dihedral : 3.825 19.156 1239 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.99 % Favored : 95.75 % Rotamer: Outliers : 4.42 % Allowed : 24.36 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.25), residues: 1153 helix: 2.65 (0.17), residues: 874 sheet: None (None), residues: 0 loop : -1.94 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 373 HIS 0.007 0.001 HIS B 499 PHE 0.043 0.002 PHE B 416 TYR 0.034 0.002 TYR B 412 ARG 0.003 0.000 ARG B 459 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 294 GLN cc_start: 0.6665 (tm-30) cc_final: 0.6262 (tm-30) REVERT: A 585 LEU cc_start: 0.4377 (mt) cc_final: 0.4106 (tp) REVERT: B 244 PHE cc_start: 0.8200 (t80) cc_final: 0.7366 (t80) REVERT: B 409 ASP cc_start: 0.6536 (p0) cc_final: 0.6276 (p0) outliers start: 31 outliers final: 27 residues processed: 159 average time/residue: 0.1644 time to fit residues: 38.6455 Evaluate side-chains 161 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 616 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 50.0000 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 70 optimal weight: 20.0000 chunk 75 optimal weight: 0.0070 chunk 54 optimal weight: 10.0000 chunk 10 optimal weight: 30.0000 chunk 87 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8637 Z= 0.230 Angle : 0.614 10.206 11823 Z= 0.325 Chirality : 0.040 0.207 1375 Planarity : 0.004 0.070 1499 Dihedral : 3.829 19.193 1239 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.08 % Favored : 95.66 % Rotamer: Outliers : 4.13 % Allowed : 25.50 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.25), residues: 1153 helix: 2.65 (0.17), residues: 873 sheet: None (None), residues: 0 loop : -1.84 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 266 HIS 0.008 0.001 HIS B 499 PHE 0.029 0.001 PHE A 511 TYR 0.032 0.002 TYR B 412 ARG 0.003 0.000 ARG B 459 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 1.006 Fit side-chains REVERT: A 294 GLN cc_start: 0.6735 (tm-30) cc_final: 0.6361 (tm-30) REVERT: A 585 LEU cc_start: 0.4403 (mt) cc_final: 0.4142 (tp) REVERT: B 244 PHE cc_start: 0.8218 (t80) cc_final: 0.7385 (t80) REVERT: B 394 PHE cc_start: 0.8139 (t80) cc_final: 0.7890 (t80) REVERT: B 508 MET cc_start: 0.6646 (mmt) cc_final: 0.6163 (mpp) outliers start: 29 outliers final: 26 residues processed: 162 average time/residue: 0.1544 time to fit residues: 37.7769 Evaluate side-chains 163 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 616 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 chunk 62 optimal weight: 80.0000 chunk 44 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 93 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 67 optimal weight: 50.0000 chunk 109 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8637 Z= 0.189 Angle : 0.609 9.921 11823 Z= 0.320 Chirality : 0.039 0.231 1375 Planarity : 0.004 0.070 1499 Dihedral : 3.774 18.348 1239 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.82 % Favored : 95.92 % Rotamer: Outliers : 3.28 % Allowed : 26.64 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.26), residues: 1153 helix: 2.73 (0.17), residues: 874 sheet: None (None), residues: 0 loop : -1.81 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 528 HIS 0.004 0.001 HIS A 587 PHE 0.054 0.001 PHE B 416 TYR 0.036 0.001 TYR B 412 ARG 0.003 0.000 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 294 GLN cc_start: 0.6836 (tm-30) cc_final: 0.6489 (tm-30) REVERT: B 244 PHE cc_start: 0.8176 (t80) cc_final: 0.7316 (t80) REVERT: B 270 ARG cc_start: 0.8215 (mmm-85) cc_final: 0.7584 (mmm-85) REVERT: B 506 ASP cc_start: 0.6647 (t0) cc_final: 0.6357 (m-30) outliers start: 23 outliers final: 22 residues processed: 154 average time/residue: 0.1591 time to fit residues: 36.2624 Evaluate side-chains 155 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 616 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 40.0000 chunk 51 optimal weight: 4.9990 chunk 75 optimal weight: 20.0000 chunk 114 optimal weight: 0.9980 chunk 105 optimal weight: 20.0000 chunk 91 optimal weight: 0.6980 chunk 9 optimal weight: 40.0000 chunk 70 optimal weight: 30.0000 chunk 55 optimal weight: 0.9990 chunk 72 optimal weight: 20.0000 chunk 97 optimal weight: 0.4980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8637 Z= 0.261 Angle : 0.640 11.148 11823 Z= 0.340 Chirality : 0.041 0.265 1375 Planarity : 0.004 0.070 1499 Dihedral : 3.894 19.507 1239 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.16 % Favored : 95.58 % Rotamer: Outliers : 3.56 % Allowed : 26.64 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.25), residues: 1153 helix: 2.60 (0.17), residues: 873 sheet: None (None), residues: 0 loop : -1.75 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 292 HIS 0.005 0.001 HIS B 313 PHE 0.028 0.002 PHE A 511 TYR 0.031 0.002 TYR B 412 ARG 0.003 0.000 ARG B 459 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: B 244 PHE cc_start: 0.8228 (t80) cc_final: 0.7391 (t80) REVERT: B 270 ARG cc_start: 0.8268 (mmm-85) cc_final: 0.7645 (mmm-85) REVERT: B 506 ASP cc_start: 0.6809 (t0) cc_final: 0.6536 (m-30) outliers start: 25 outliers final: 23 residues processed: 150 average time/residue: 0.1559 time to fit residues: 35.2730 Evaluate side-chains 158 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 583 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 11 optimal weight: 50.0000 chunk 16 optimal weight: 50.0000 chunk 80 optimal weight: 0.9990 chunk 5 optimal weight: 50.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.195447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.152164 restraints weight = 17741.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.148796 restraints weight = 11417.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.149820 restraints weight = 11244.998| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8637 Z= 0.220 Angle : 0.637 14.977 11823 Z= 0.332 Chirality : 0.040 0.245 1375 Planarity : 0.004 0.069 1499 Dihedral : 3.842 18.536 1239 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.99 % Favored : 95.75 % Rotamer: Outliers : 3.56 % Allowed : 27.07 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.25), residues: 1153 helix: 2.65 (0.17), residues: 873 sheet: None (None), residues: 0 loop : -1.82 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 292 HIS 0.004 0.001 HIS B 499 PHE 0.016 0.001 PHE B 487 TYR 0.030 0.001 TYR B 412 ARG 0.003 0.000 ARG B 459 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1699.70 seconds wall clock time: 31 minutes 46.62 seconds (1906.62 seconds total)