Starting phenix.real_space_refine on Thu Mar 13 05:39:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xvz_38724/03_2025/8xvz_38724.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xvz_38724/03_2025/8xvz_38724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xvz_38724/03_2025/8xvz_38724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xvz_38724/03_2025/8xvz_38724.map" model { file = "/net/cci-nas-00/data/ceres_data/8xvz_38724/03_2025/8xvz_38724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xvz_38724/03_2025/8xvz_38724.cif" } resolution = 3.78 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= 0.008 sd= 0.059 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 26 5.16 5 C 5745 2.51 5 N 1389 2.21 5 O 1530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8690 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 4438 Classifications: {'peptide': 622} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'PTRANS': 29, 'TRANS': 592} Chain breaks: 3 Unresolved non-hydrogen bonds: 600 Unresolved non-hydrogen angles: 750 Unresolved non-hydrogen dihedrals: 519 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 7, 'ASN:plan1': 5, 'TRP:plan': 4, 'ASP:plan': 4, 'PHE:plan': 10, 'GLU:plan': 19, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 359 Chain: "B" Number of atoms: 4252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4252 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 141} Link IDs: {'CIS': 1, 'PTRANS': 27, 'TRANS': 572} Chain breaks: 4 Unresolved non-hydrogen bonds: 618 Unresolved non-hydrogen angles: 773 Unresolved non-hydrogen dihedrals: 535 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 4, 'ASP:plan': 4, 'PHE:plan': 10, 'GLU:plan': 20, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 375 Time building chain proxies: 5.38, per 1000 atoms: 0.62 Number of scatterers: 8690 At special positions: 0 Unit cell: (75.96, 133.985, 98.115, 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 26 16.00 O 1530 8.00 N 1389 7.00 C 5745 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 1.1 seconds 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2338 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 2 sheets defined 68.6% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 3 through 26 removed outlier: 4.132A pdb=" N LEU A 7 " --> pdb=" O PHE A 3 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 42 Processing helix chain 'A' and resid 56 through 67 removed outlier: 3.562A pdb=" N TRP A 61 " --> pdb=" O ASN A 57 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG A 63 " --> pdb=" O PHE A 59 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 78 through 98 removed outlier: 3.791A pdb=" N ALA A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 151 through 185 removed outlier: 4.101A pdb=" N SER A 175 " --> pdb=" O TYR A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 220 Processing helix chain 'A' and resid 233 through 248 Processing helix chain 'A' and resid 291 through 305 removed outlier: 3.516A pdb=" N GLU A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 326 Processing helix chain 'A' and resid 355 through 378 removed outlier: 3.524A pdb=" N ARG A 359 " --> pdb=" O LYS A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 388 Processing helix chain 'A' and resid 390 through 395 removed outlier: 3.696A pdb=" N ARG A 395 " --> pdb=" O LYS A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 405 removed outlier: 5.269A pdb=" N LYS A 401 " --> pdb=" O PRO A 398 " (cutoff:3.500A) Proline residue: A 402 - end of helix Processing helix chain 'A' and resid 409 through 439 removed outlier: 3.898A pdb=" N LEU A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) Proline residue: A 418 - end of helix Proline residue: A 430 - end of helix removed outlier: 3.569A pdb=" N LEU A 436 " --> pdb=" O LEU A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 465 Processing helix chain 'A' and resid 465 through 476 Processing helix chain 'A' and resid 489 through 525 Proline residue: A 499 - end of helix Processing helix chain 'A' and resid 525 through 537 removed outlier: 3.539A pdb=" N LYS A 533 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 534 " --> pdb=" O PHE A 530 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS A 535 " --> pdb=" O HIS A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 572 removed outlier: 3.530A pdb=" N GLY A 561 " --> pdb=" O THR A 557 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE A 565 " --> pdb=" O GLY A 561 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU A 566 " --> pdb=" O ASP A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 578 No H-bonds generated for 'chain 'A' and resid 576 through 578' Processing helix chain 'A' and resid 579 through 596 Processing helix chain 'A' and resid 612 through 637 removed outlier: 3.515A pdb=" N ILE A 616 " --> pdb=" O MET A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 662 Processing helix chain 'A' and resid 672 through 679 removed outlier: 3.656A pdb=" N GLU A 679 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 694 removed outlier: 3.854A pdb=" N ARG A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ALA A 692 " --> pdb=" O GLU A 688 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR A 693 " --> pdb=" O ILE A 689 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 694 " --> pdb=" O PHE A 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 27 removed outlier: 3.737A pdb=" N VAL B 8 " --> pdb=" O GLY B 4 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU B 27 " --> pdb=" O LEU B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 33 removed outlier: 3.671A pdb=" N SER B 31 " --> pdb=" O SER B 28 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY B 32 " --> pdb=" O ARG B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 77 removed outlier: 3.967A pdb=" N VAL B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 98 removed outlier: 3.695A pdb=" N ALA B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 107 removed outlier: 3.602A pdb=" N LEU B 106 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 184 removed outlier: 3.566A pdb=" N PHE B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER B 184 " --> pdb=" O GLN B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 220 Processing helix chain 'B' and resid 237 through 250 removed outlier: 3.530A pdb=" N LEU B 250 " --> pdb=" O TYR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 303 Processing helix chain 'B' and resid 317 through 326 removed outlier: 3.797A pdb=" N GLN B 326 " --> pdb=" O ALA B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 347 removed outlier: 3.717A pdb=" N LEU B 347 " --> pdb=" O PRO B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 379 removed outlier: 3.737A pdb=" N ILE B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 386 Processing helix chain 'B' and resid 411 through 428 Proline residue: B 418 - end of helix removed outlier: 3.743A pdb=" N MET B 428 " --> pdb=" O VAL B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 439 Processing helix chain 'B' and resid 444 through 477 removed outlier: 4.270A pdb=" N ARG B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 513 Proline residue: B 499 - end of helix removed outlier: 4.454A pdb=" N LEU B 506 " --> pdb=" O ALA B 502 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL B 509 " --> pdb=" O PHE B 505 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA B 510 " --> pdb=" O LEU B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 523 removed outlier: 3.578A pdb=" N SER B 522 " --> pdb=" O GLY B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 536 Processing helix chain 'B' and resid 560 through 571 removed outlier: 4.316A pdb=" N ILE B 565 " --> pdb=" O GLY B 561 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU B 566 " --> pdb=" O ASP B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 601 removed outlier: 4.013A pdb=" N LEU B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 638 Processing helix chain 'B' and resid 642 through 664 Proline residue: B 648 - end of helix Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 685 through 692 removed outlier: 3.884A pdb=" N ILE B 689 " --> pdb=" O ASP B 685 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 193 through 194 removed outlier: 3.590A pdb=" N VAL A 313 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ALA A 310 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 194 through 196 removed outlier: 3.680A pdb=" N ARG B 226 " --> pdb=" O PHE B 314 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1698 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: 2.37 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1517 1.32 - 1.45: 2333 1.45 - 1.57: 5019 1.57 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 8909 Sorted by residual: bond pdb=" CB VAL A 313 " pdb=" CG2 VAL A 313 " ideal model delta sigma weight residual 1.521 1.439 0.082 3.30e-02 9.18e+02 6.15e+00 bond pdb=" C ASN A 596 " pdb=" O ASN A 596 " ideal model delta sigma weight residual 1.234 1.202 0.033 1.38e-02 5.25e+03 5.64e+00 bond pdb=" CB VAL B 15 " pdb=" CG2 VAL B 15 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.64e+00 bond pdb=" CB GLU A 619 " pdb=" CG GLU A 619 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.63e+00 bond pdb=" CB TRP A 336 " pdb=" CG TRP A 336 " ideal model delta sigma weight residual 1.498 1.432 0.066 3.10e-02 1.04e+03 4.49e+00 ... (remaining 8904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 11823 2.58 - 5.15: 360 5.15 - 7.73: 47 7.73 - 10.31: 6 10.31 - 12.89: 3 Bond angle restraints: 12239 Sorted by residual: angle pdb=" N ASN B 237 " pdb=" CA ASN B 237 " pdb=" C ASN B 237 " ideal model delta sigma weight residual 113.18 102.45 10.73 1.33e+00 5.65e-01 6.50e+01 angle pdb=" CA ASN B 237 " pdb=" C ASN B 237 " pdb=" N LYS B 238 " ideal model delta sigma weight residual 118.22 113.55 4.67 1.03e+00 9.43e-01 2.06e+01 angle pdb=" N ILE A 525 " pdb=" CA ILE A 525 " pdb=" C ILE A 525 " ideal model delta sigma weight residual 112.35 117.58 -5.23 1.20e+00 6.94e-01 1.90e+01 angle pdb=" CG1 ILE A 379 " pdb=" CB ILE A 379 " pdb=" CG2 ILE A 379 " ideal model delta sigma weight residual 110.70 97.81 12.89 3.00e+00 1.11e-01 1.85e+01 angle pdb=" C MET A 378 " pdb=" N ILE A 379 " pdb=" CA ILE A 379 " ideal model delta sigma weight residual 122.13 129.60 -7.47 1.85e+00 2.92e-01 1.63e+01 ... (remaining 12234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4750 17.96 - 35.91: 323 35.91 - 53.87: 57 53.87 - 71.83: 5 71.83 - 89.78: 7 Dihedral angle restraints: 5142 sinusoidal: 1547 harmonic: 3595 Sorted by residual: dihedral pdb=" CA LYS B 235 " pdb=" C LYS B 235 " pdb=" N VAL B 236 " pdb=" CA VAL B 236 " ideal model delta harmonic sigma weight residual -180.00 -106.14 -73.86 0 5.00e+00 4.00e-02 2.18e+02 dihedral pdb=" CA VAL B 236 " pdb=" C VAL B 236 " pdb=" N ASN B 237 " pdb=" CA ASN B 237 " ideal model delta harmonic sigma weight residual 180.00 126.39 53.61 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" CA PHE B 513 " pdb=" C PHE B 513 " pdb=" N PHE B 514 " pdb=" CA PHE B 514 " ideal model delta harmonic sigma weight residual -180.00 -130.36 -49.64 0 5.00e+00 4.00e-02 9.85e+01 ... (remaining 5139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1127 0.059 - 0.117: 338 0.117 - 0.176: 42 0.176 - 0.234: 6 0.234 - 0.293: 3 Chirality restraints: 1516 Sorted by residual: chirality pdb=" CG LEU B 22 " pdb=" CB LEU B 22 " pdb=" CD1 LEU B 22 " pdb=" CD2 LEU B 22 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB ILE A 379 " pdb=" CA ILE A 379 " pdb=" CG1 ILE A 379 " pdb=" CG2 ILE A 379 " both_signs ideal model delta sigma weight residual False 2.64 2.92 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CB VAL A 313 " pdb=" CA VAL A 313 " pdb=" CG1 VAL A 313 " pdb=" CG2 VAL A 313 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 1513 not shown) Planarity restraints: 1520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 336 " -0.024 2.00e-02 2.50e+03 5.05e-02 6.37e+01 pdb=" CG TRP A 336 " 0.116 2.00e-02 2.50e+03 pdb=" CD1 TRP A 336 " -0.099 2.00e-02 2.50e+03 pdb=" CD2 TRP A 336 " 0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP A 336 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TRP A 336 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 336 " -0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 336 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 336 " -0.025 2.00e-02 2.50e+03 pdb=" CH2 TRP A 336 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 525 " -0.075 5.00e-02 4.00e+02 1.12e-01 1.99e+01 pdb=" N PRO A 526 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO A 526 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 526 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 171 " 0.036 2.00e-02 2.50e+03 2.95e-02 1.74e+01 pdb=" CG TYR A 171 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 TYR A 171 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 171 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 171 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 171 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR A 171 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 171 " -0.000 2.00e-02 2.50e+03 ... (remaining 1517 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 87 2.56 - 3.14: 8262 3.14 - 3.73: 13565 3.73 - 4.31: 17219 4.31 - 4.90: 28035 Nonbonded interactions: 67168 Sorted by model distance: nonbonded pdb=" O VAL A 593 " pdb=" O ASN A 596 " model vdw 1.969 3.040 nonbonded pdb=" OH TYR A 157 " pdb=" O LEU A 645 " model vdw 2.118 3.040 nonbonded pdb=" OE2 GLU B 343 " pdb=" OG SER B 446 " model vdw 2.141 3.040 nonbonded pdb=" OH TYR B 157 " pdb=" O LEU B 645 " model vdw 2.147 3.040 nonbonded pdb=" OG1 THR A 207 " pdb=" OE1 GLU A 210 " model vdw 2.170 3.040 ... (remaining 67163 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 3 through 388 or (resid 410 and (name N or name CA or name \ C or name O or name CB )) or resid 411 through 413 or (resid 414 and (name N or \ name CA or name C or name O or name CB )) or resid 415 through 664 or (resid 66 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 666 through \ 696)) 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.470 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 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 : 0.011 0.082 8909 Z= 0.699 Angle : 1.046 12.887 12239 Z= 0.576 Chirality : 0.054 0.293 1516 Planarity : 0.008 0.112 1520 Dihedral : 13.535 89.783 2804 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.33 % Allowed : 16.18 % Favored : 83.49 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 5.36 % Twisted General : 0.60 % 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: -2.09 (0.24), residues: 1205 helix: -0.02 (0.19), residues: 762 sheet: -2.57 (1.12), residues: 26 loop : -4.02 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.116 0.005 TRP A 336 HIS 0.007 0.002 HIS A 617 PHE 0.041 0.003 PHE A 640 TYR 0.072 0.003 TYR A 171 ARG 0.007 0.001 ARG B 661 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.976 Fit side-chains REVERT: A 465 PHE cc_start: 0.7191 (t80) cc_final: 0.6981 (t80) REVERT: B 618 GLN cc_start: 0.8411 (tm-30) cc_final: 0.8109 (tm-30) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1716 time to fit residues: 42.2847 Evaluate side-chains 142 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 0.0970 chunk 58 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN B 351 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.145959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.112334 restraints weight = 15347.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.114738 restraints weight = 9621.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.116002 restraints weight = 7211.297| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8909 Z= 0.246 Angle : 0.805 14.782 12239 Z= 0.422 Chirality : 0.044 0.226 1516 Planarity : 0.007 0.098 1520 Dihedral : 7.207 71.742 1271 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.33 % Allowed : 13.36 % Favored : 86.31 % Rotamer: Outliers : 2.04 % Allowed : 11.72 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 5.36 % Twisted General : 0.43 % 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: -1.39 (0.25), residues: 1205 helix: 0.43 (0.19), residues: 791 sheet: -1.22 (1.77), residues: 12 loop : -3.81 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 336 HIS 0.005 0.001 HIS B 615 PHE 0.036 0.002 PHE B 513 TYR 0.036 0.002 TYR A 171 ARG 0.005 0.001 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.908 Fit side-chains REVERT: A 215 TYR cc_start: 0.8322 (t80) cc_final: 0.8066 (t80) REVERT: A 374 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7959 (mp) REVERT: A 378 MET cc_start: 0.4502 (OUTLIER) cc_final: 0.3816 (tmm) REVERT: A 437 SER cc_start: 0.9118 (m) cc_final: 0.8553 (p) REVERT: B 210 GLU cc_start: 0.8636 (pm20) cc_final: 0.8295 (pm20) REVERT: B 447 HIS cc_start: 0.8876 (m90) cc_final: 0.8528 (m170) REVERT: B 618 GLN cc_start: 0.8274 (tm-30) cc_final: 0.7813 (tm-30) outliers start: 16 outliers final: 6 residues processed: 175 average time/residue: 0.1630 time to fit residues: 41.9269 Evaluate side-chains 154 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 601 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 39 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.146973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.113080 restraints weight = 15680.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.115490 restraints weight = 9815.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.116967 restraints weight = 7353.366| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8909 Z= 0.239 Angle : 0.761 13.743 12239 Z= 0.397 Chirality : 0.043 0.180 1516 Planarity : 0.006 0.102 1520 Dihedral : 6.819 70.249 1271 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.33 % Allowed : 13.11 % Favored : 86.56 % Rotamer: Outliers : 3.57 % Allowed : 17.07 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 3.57 % Twisted General : 0.52 % 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: -1.15 (0.25), residues: 1205 helix: 0.57 (0.19), residues: 798 sheet: 0.43 (1.83), residues: 10 loop : -3.71 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 336 HIS 0.005 0.001 HIS B 615 PHE 0.044 0.002 PHE B 513 TYR 0.030 0.001 TYR A 171 ARG 0.003 0.000 ARG B 661 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 GLU cc_start: 0.8501 (pp20) cc_final: 0.8208 (pp20) REVERT: A 378 MET cc_start: 0.4360 (OUTLIER) cc_final: 0.3633 (tmm) REVERT: A 425 PHE cc_start: 0.7696 (t80) cc_final: 0.7324 (t80) REVERT: A 437 SER cc_start: 0.9111 (m) cc_final: 0.8534 (p) REVERT: A 620 ILE cc_start: 0.8071 (tt) cc_final: 0.7709 (tp) REVERT: B 72 ASP cc_start: 0.8303 (t0) cc_final: 0.8043 (t0) REVERT: B 369 PHE cc_start: 0.8300 (t80) cc_final: 0.8052 (t80) REVERT: B 416 PHE cc_start: 0.7664 (OUTLIER) cc_final: 0.7368 (t80) REVERT: B 447 HIS cc_start: 0.8891 (m90) cc_final: 0.8559 (m170) REVERT: B 618 GLN cc_start: 0.8380 (tm-30) cc_final: 0.8012 (tm-30) REVERT: B 649 LEU cc_start: 0.8792 (mt) cc_final: 0.8588 (mt) outliers start: 28 outliers final: 11 residues processed: 181 average time/residue: 0.1636 time to fit residues: 44.1598 Evaluate side-chains 163 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 458 TYR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 572 TYR Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 601 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 chunk 15 optimal weight: 0.0000 chunk 95 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.146453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.110387 restraints weight = 15608.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.113304 restraints weight = 8949.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.114943 restraints weight = 6367.011| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8909 Z= 0.241 Angle : 0.760 12.933 12239 Z= 0.392 Chirality : 0.044 0.232 1516 Planarity : 0.006 0.103 1520 Dihedral : 6.661 69.590 1271 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.33 % Allowed : 12.61 % Favored : 87.05 % Rotamer: Outliers : 2.55 % Allowed : 20.64 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 3.57 % Twisted General : 0.43 % 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: -1.07 (0.25), residues: 1205 helix: 0.61 (0.19), residues: 796 sheet: 0.13 (1.74), residues: 10 loop : -3.60 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 336 HIS 0.006 0.001 HIS B 615 PHE 0.040 0.002 PHE B 513 TYR 0.023 0.001 TYR A 171 ARG 0.003 0.000 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 1.050 Fit side-chains REVERT: A 190 GLU cc_start: 0.8492 (pp20) cc_final: 0.8267 (pp20) REVERT: A 308 GLN cc_start: 0.8361 (mm-40) cc_final: 0.7217 (mm-40) REVERT: A 353 ASN cc_start: 0.8605 (t0) cc_final: 0.8380 (m-40) REVERT: A 378 MET cc_start: 0.4377 (tmm) cc_final: 0.3685 (tmm) REVERT: A 425 PHE cc_start: 0.7551 (t80) cc_final: 0.7226 (t80) REVERT: A 437 SER cc_start: 0.9060 (m) cc_final: 0.8489 (p) REVERT: B 72 ASP cc_start: 0.8385 (t0) cc_final: 0.8111 (t0) REVERT: B 308 GLN cc_start: 0.7482 (mt0) cc_final: 0.6665 (mp10) REVERT: B 369 PHE cc_start: 0.8318 (t80) cc_final: 0.8113 (t80) REVERT: B 376 PHE cc_start: 0.8203 (t80) cc_final: 0.7915 (t80) REVERT: B 416 PHE cc_start: 0.7688 (OUTLIER) cc_final: 0.7378 (t80) REVERT: B 447 HIS cc_start: 0.8904 (m90) cc_final: 0.8572 (m170) REVERT: B 618 GLN cc_start: 0.8386 (tm-30) cc_final: 0.8005 (tm-30) outliers start: 20 outliers final: 11 residues processed: 172 average time/residue: 0.1602 time to fit residues: 40.7824 Evaluate side-chains 157 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 458 TYR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 601 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 71 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 68 optimal weight: 0.0980 chunk 82 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 353 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 = 0.3784 r_free = 0.3784 target = 0.146905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.111336 restraints weight = 15596.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.113989 restraints weight = 9483.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.115675 restraints weight = 6984.945| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 8909 Z= 0.247 Angle : 0.759 13.491 12239 Z= 0.390 Chirality : 0.043 0.196 1516 Planarity : 0.006 0.104 1520 Dihedral : 6.557 68.671 1271 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.33 % Allowed : 13.03 % Favored : 86.64 % Rotamer: Outliers : 3.18 % Allowed : 22.29 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 3.57 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.25), residues: 1205 helix: 0.67 (0.19), residues: 801 sheet: -0.00 (1.74), residues: 10 loop : -3.53 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 336 HIS 0.006 0.001 HIS B 615 PHE 0.045 0.002 PHE B 513 TYR 0.021 0.001 TYR A 171 ARG 0.002 0.000 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 TRP cc_start: 0.7503 (m-10) cc_final: 0.7230 (m-10) REVERT: A 378 MET cc_start: 0.4370 (OUTLIER) cc_final: 0.3891 (tmm) REVERT: A 425 PHE cc_start: 0.7563 (t80) cc_final: 0.7257 (t80) REVERT: A 437 SER cc_start: 0.9058 (m) cc_final: 0.8486 (p) REVERT: B 72 ASP cc_start: 0.8367 (t0) cc_final: 0.8096 (t0) REVERT: B 308 GLN cc_start: 0.6965 (mt0) cc_final: 0.6726 (mt0) REVERT: B 376 PHE cc_start: 0.8263 (t80) cc_final: 0.7945 (t80) REVERT: B 416 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.7373 (t80) REVERT: B 447 HIS cc_start: 0.8901 (m90) cc_final: 0.8570 (m170) REVERT: B 618 GLN cc_start: 0.8380 (tm-30) cc_final: 0.7996 (tm-30) outliers start: 25 outliers final: 17 residues processed: 171 average time/residue: 0.1765 time to fit residues: 45.0343 Evaluate side-chains 165 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 458 TYR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 377 TYR Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 601 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 33 optimal weight: 20.0000 chunk 58 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 46 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.145874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.109391 restraints weight = 15620.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.112213 restraints weight = 9091.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.114041 restraints weight = 6525.639| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8909 Z= 0.296 Angle : 0.776 13.146 12239 Z= 0.400 Chirality : 0.044 0.192 1516 Planarity : 0.006 0.104 1520 Dihedral : 6.562 68.012 1271 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.45 % Favored : 87.30 % Rotamer: Outliers : 3.82 % Allowed : 23.82 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 3.57 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.26), residues: 1205 helix: 0.69 (0.19), residues: 800 sheet: -2.03 (1.16), residues: 24 loop : -3.55 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 336 HIS 0.005 0.001 HIS B 617 PHE 0.044 0.002 PHE B 513 TYR 0.021 0.001 TYR A 171 ARG 0.002 0.000 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 TRP cc_start: 0.7702 (m-10) cc_final: 0.7259 (m-10) REVERT: A 369 PHE cc_start: 0.8903 (t80) cc_final: 0.8683 (t80) REVERT: A 378 MET cc_start: 0.4386 (OUTLIER) cc_final: 0.3715 (tmm) REVERT: A 425 PHE cc_start: 0.7491 (t80) cc_final: 0.7222 (t80) REVERT: A 437 SER cc_start: 0.9089 (m) cc_final: 0.8497 (p) REVERT: A 572 TYR cc_start: 0.8620 (m-10) cc_final: 0.8346 (m-10) REVERT: A 620 ILE cc_start: 0.8054 (tt) cc_final: 0.7558 (tp) REVERT: B 72 ASP cc_start: 0.8477 (t0) cc_final: 0.8191 (t0) REVERT: B 447 HIS cc_start: 0.8957 (m90) cc_final: 0.8582 (m170) REVERT: B 618 GLN cc_start: 0.8462 (tm-30) cc_final: 0.8096 (tm-30) outliers start: 30 outliers final: 18 residues processed: 173 average time/residue: 0.1797 time to fit residues: 46.1867 Evaluate side-chains 163 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 458 TYR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 377 TYR Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 601 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 97 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 114 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.147658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.111978 restraints weight = 15636.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.114634 restraints weight = 9530.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.116351 restraints weight = 6976.485| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8909 Z= 0.230 Angle : 0.756 12.513 12239 Z= 0.386 Chirality : 0.043 0.199 1516 Planarity : 0.006 0.105 1520 Dihedral : 6.429 67.268 1271 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.61 % Favored : 87.14 % Rotamer: Outliers : 3.44 % Allowed : 24.97 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 3.57 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.25), residues: 1205 helix: 0.79 (0.19), residues: 796 sheet: -1.50 (1.22), residues: 22 loop : -3.56 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 548 HIS 0.004 0.001 HIS B 615 PHE 0.042 0.001 PHE B 513 TYR 0.020 0.001 TYR A 364 ARG 0.005 0.000 ARG B 661 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 GLU cc_start: 0.8198 (pt0) cc_final: 0.7969 (pt0) REVERT: A 336 TRP cc_start: 0.7624 (m-10) cc_final: 0.7368 (m-10) REVERT: A 378 MET cc_start: 0.4368 (OUTLIER) cc_final: 0.3670 (tmm) REVERT: A 437 SER cc_start: 0.9044 (m) cc_final: 0.8452 (p) REVERT: A 572 TYR cc_start: 0.8570 (m-10) cc_final: 0.8273 (m-10) REVERT: A 620 ILE cc_start: 0.7997 (tt) cc_final: 0.7482 (tp) REVERT: B 72 ASP cc_start: 0.8449 (t0) cc_final: 0.8160 (t0) REVERT: B 231 THR cc_start: 0.7834 (OUTLIER) cc_final: 0.7509 (p) REVERT: B 416 PHE cc_start: 0.7684 (OUTLIER) cc_final: 0.7477 (t80) REVERT: B 447 HIS cc_start: 0.8924 (m90) cc_final: 0.8589 (m170) REVERT: B 618 GLN cc_start: 0.8211 (tm-30) cc_final: 0.7893 (tm-30) outliers start: 27 outliers final: 17 residues processed: 173 average time/residue: 0.1877 time to fit residues: 48.2372 Evaluate side-chains 166 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 416 PHE Chi-restraints excluded: chain A residue 458 TYR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 463 ASN Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 601 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 8 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 41 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 90 optimal weight: 0.0570 chunk 115 optimal weight: 0.9980 chunk 62 optimal weight: 20.0000 chunk 85 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.148898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.113312 restraints weight = 15586.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.115992 restraints weight = 9422.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.117483 restraints weight = 6886.863| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8909 Z= 0.220 Angle : 0.750 13.972 12239 Z= 0.380 Chirality : 0.043 0.229 1516 Planarity : 0.006 0.106 1520 Dihedral : 6.271 66.116 1271 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.03 % Favored : 87.72 % Rotamer: Outliers : 2.68 % Allowed : 25.73 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 3.57 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.25), residues: 1205 helix: 0.87 (0.19), residues: 798 sheet: -1.86 (1.14), residues: 22 loop : -3.53 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 548 HIS 0.005 0.001 HIS B 615 PHE 0.041 0.001 PHE B 513 TYR 0.020 0.001 TYR A 364 ARG 0.005 0.000 ARG B 661 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.8262 (mmt) cc_final: 0.7769 (mmt) REVERT: A 336 TRP cc_start: 0.7687 (m-10) cc_final: 0.7187 (m-10) REVERT: A 378 MET cc_start: 0.4334 (OUTLIER) cc_final: 0.3670 (tmm) REVERT: A 437 SER cc_start: 0.9016 (m) cc_final: 0.8450 (p) REVERT: A 572 TYR cc_start: 0.8619 (m-10) cc_final: 0.8347 (m-10) REVERT: A 620 ILE cc_start: 0.8138 (tt) cc_final: 0.7621 (tp) REVERT: B 72 ASP cc_start: 0.8333 (t0) cc_final: 0.8044 (t0) REVERT: B 210 GLU cc_start: 0.8664 (pm20) cc_final: 0.8441 (pm20) REVERT: B 351 ASN cc_start: 0.8928 (t0) cc_final: 0.8272 (t0) REVERT: B 447 HIS cc_start: 0.8907 (m90) cc_final: 0.8585 (m170) REVERT: B 618 GLN cc_start: 0.8326 (tm-30) cc_final: 0.7987 (tm-30) REVERT: B 661 ARG cc_start: 0.7247 (tpt170) cc_final: 0.6905 (tpt170) outliers start: 21 outliers final: 17 residues processed: 171 average time/residue: 0.1493 time to fit residues: 38.4575 Evaluate side-chains 168 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 458 TYR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 377 TYR Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 601 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 41 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 120 optimal weight: 0.0670 chunk 73 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 11 optimal weight: 0.0980 chunk 79 optimal weight: 0.4980 chunk 97 optimal weight: 2.9990 chunk 50 optimal weight: 0.3980 overall best weight: 0.3718 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.151387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.115649 restraints weight = 15641.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.118360 restraints weight = 9473.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.119870 restraints weight = 6943.386| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8909 Z= 0.206 Angle : 0.755 13.749 12239 Z= 0.380 Chirality : 0.043 0.239 1516 Planarity : 0.006 0.106 1520 Dihedral : 6.149 63.864 1271 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.12 % Favored : 87.63 % Rotamer: Outliers : 2.55 % Allowed : 26.24 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 3.57 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.25), residues: 1205 helix: 0.89 (0.19), residues: 792 sheet: -1.83 (1.14), residues: 22 loop : -3.44 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 548 HIS 0.005 0.001 HIS B 615 PHE 0.042 0.001 PHE B 513 TYR 0.020 0.001 TYR A 364 ARG 0.004 0.000 ARG B 661 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.8183 (mmt) cc_final: 0.7799 (mmt) REVERT: A 336 TRP cc_start: 0.7588 (m-10) cc_final: 0.7086 (m-10) REVERT: A 369 PHE cc_start: 0.8827 (t80) cc_final: 0.8578 (t80) REVERT: A 378 MET cc_start: 0.4346 (OUTLIER) cc_final: 0.3713 (tmm) REVERT: A 436 LEU cc_start: 0.8920 (mp) cc_final: 0.8476 (mt) REVERT: A 437 SER cc_start: 0.8994 (m) cc_final: 0.8394 (p) REVERT: A 572 TYR cc_start: 0.8659 (m-10) cc_final: 0.8446 (m-10) REVERT: A 620 ILE cc_start: 0.8076 (tt) cc_final: 0.7487 (tp) REVERT: B 72 ASP cc_start: 0.8241 (t0) cc_final: 0.7954 (t0) REVERT: B 351 ASN cc_start: 0.8916 (t0) cc_final: 0.8329 (t0) REVERT: B 376 PHE cc_start: 0.8394 (t80) cc_final: 0.8062 (t80) REVERT: B 447 HIS cc_start: 0.8878 (m90) cc_final: 0.8598 (m170) REVERT: B 563 MET cc_start: 0.8637 (ttt) cc_final: 0.8421 (ttp) REVERT: B 618 GLN cc_start: 0.8378 (tm-30) cc_final: 0.8016 (tm-30) outliers start: 20 outliers final: 19 residues processed: 175 average time/residue: 0.2201 time to fit residues: 59.2811 Evaluate side-chains 178 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 458 TYR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 463 ASN Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 601 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 92 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 66 optimal weight: 20.0000 chunk 23 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 24 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.150496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.115050 restraints weight = 15458.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.117725 restraints weight = 9369.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.119398 restraints weight = 6845.758| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8909 Z= 0.229 Angle : 0.779 16.011 12239 Z= 0.387 Chirality : 0.044 0.261 1516 Planarity : 0.006 0.106 1520 Dihedral : 6.104 63.414 1271 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.33 % Allowed : 12.37 % Favored : 87.30 % Rotamer: Outliers : 2.80 % Allowed : 26.37 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 3.57 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.25), residues: 1205 helix: 0.96 (0.19), residues: 795 sheet: -1.76 (1.17), residues: 22 loop : -3.41 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 548 HIS 0.004 0.001 HIS B 615 PHE 0.042 0.001 PHE B 513 TYR 0.019 0.001 TYR A 364 ARG 0.005 0.000 ARG B 661 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2410 Ramachandran restraints generated. 1205 Oldfield, 0 Emsley, 1205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 PHE cc_start: 0.8758 (t80) cc_final: 0.8284 (t80) REVERT: A 378 MET cc_start: 0.4325 (OUTLIER) cc_final: 0.3681 (tmm) REVERT: A 437 SER cc_start: 0.9000 (m) cc_final: 0.8434 (p) REVERT: A 620 ILE cc_start: 0.8140 (tt) cc_final: 0.7572 (tp) REVERT: B 72 ASP cc_start: 0.8271 (t0) cc_final: 0.7980 (t0) REVERT: B 105 THR cc_start: 0.8430 (m) cc_final: 0.8200 (m) REVERT: B 351 ASN cc_start: 0.8940 (OUTLIER) cc_final: 0.8271 (t0) REVERT: B 376 PHE cc_start: 0.8381 (t80) cc_final: 0.8058 (t80) REVERT: B 381 ILE cc_start: 0.8121 (mm) cc_final: 0.7846 (mm) REVERT: B 447 HIS cc_start: 0.8912 (m90) cc_final: 0.8608 (m170) REVERT: B 618 GLN cc_start: 0.8374 (tm-30) cc_final: 0.8006 (tm-30) outliers start: 22 outliers final: 19 residues processed: 175 average time/residue: 0.1526 time to fit residues: 40.3255 Evaluate side-chains 182 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 458 TYR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 463 ASN Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 601 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 18 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 64 optimal weight: 0.2980 chunk 55 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.150088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.113743 restraints weight = 15820.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.116653 restraints weight = 9251.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.118490 restraints weight = 6634.214| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 8909 Z= 0.263 Angle : 1.048 59.187 12239 Z= 0.583 Chirality : 0.045 0.508 1516 Planarity : 0.006 0.106 1520 Dihedral : 6.201 63.465 1271 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.41 % Allowed : 12.28 % Favored : 87.30 % Rotamer: Outliers : 2.93 % Allowed : 26.62 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 3.57 % Twisted General : 0.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.25), residues: 1205 helix: 0.97 (0.19), residues: 795 sheet: -1.76 (1.16), residues: 22 loop : -3.39 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 336 HIS 0.004 0.001 HIS B 615 PHE 0.042 0.001 PHE B 513 TYR 0.018 0.001 TYR A 364 ARG 0.006 0.000 ARG B 661 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2660.74 seconds wall clock time: 48 minutes 49.44 seconds (2929.44 seconds total)