Starting phenix.real_space_refine on Fri Jan 19 07:43:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqe_13591/01_2024/7pqe_13591.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqe_13591/01_2024/7pqe_13591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqe_13591/01_2024/7pqe_13591.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqe_13591/01_2024/7pqe_13591.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqe_13591/01_2024/7pqe_13591.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqe_13591/01_2024/7pqe_13591.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 Mg 1 5.21 5 S 35 5.16 5 C 6833 2.51 5 N 1828 2.21 5 O 2048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A GLU 378": "OE1" <-> "OE2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "A ARG 431": "NH1" <-> "NH2" Residue "A GLU 439": "OE1" <-> "OE2" Residue "A ARG 475": "NH1" <-> "NH2" Residue "A GLU 545": "OE1" <-> "OE2" Residue "A ARG 557": "NH1" <-> "NH2" Residue "A ARG 559": "NH1" <-> "NH2" Residue "A ARG 766": "NH1" <-> "NH2" Residue "A GLU 791": "OE1" <-> "OE2" Residue "A GLU 869": "OE1" <-> "OE2" Residue "A GLU 888": "OE1" <-> "OE2" Residue "A PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 142": "OE1" <-> "OE2" Residue "C TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 295": "NH1" <-> "NH2" Residue "C TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 396": "OD1" <-> "OD2" Residue "C ASP 437": "OD1" <-> "OD2" Residue "C GLU 439": "OE1" <-> "OE2" Residue "C TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 627": "OD1" <-> "OD2" Residue "C TYR 809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 811": "OE1" <-> "OE2" Residue "B GLU 8": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B GLU 15": "OE1" <-> "OE2" Residue "B PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 10746 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3870 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 22, 'TRANS': 469} Chain breaks: 3 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "C" Number of atoms: 5995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 739, 5995 Classifications: {'peptide': 739} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 31, 'TRANS': 707} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 879 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 144 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.91, per 1000 atoms: 0.55 Number of scatterers: 10746 At special positions: 0 Unit cell: (140.209, 102.569, 94.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 35 16.00 Mg 1 11.99 O 2048 8.00 N 1828 7.00 C 6833 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.31 Conformation dependent library (CDL) restraints added in 2.0 seconds 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2584 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 12 sheets defined 55.5% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 239 through 251 Processing helix chain 'A' and resid 278 through 303 Processing helix chain 'A' and resid 314 through 318 Processing helix chain 'A' and resid 319 through 332 removed outlier: 4.428A pdb=" N PHE A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 365 Processing helix chain 'A' and resid 366 through 369 Processing helix chain 'A' and resid 376 through 389 Processing helix chain 'A' and resid 397 through 410 removed outlier: 4.066A pdb=" N ILE A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP A 410 " --> pdb=" O GLY A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 431 removed outlier: 3.827A pdb=" N PHE A 421 " --> pdb=" O PRO A 417 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 452 Processing helix chain 'A' and resid 515 through 521 Processing helix chain 'A' and resid 544 through 553 Processing helix chain 'A' and resid 554 through 561 removed outlier: 4.006A pdb=" N ALA A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 587 Proline residue: A 582 - end of helix Processing helix chain 'A' and resid 771 through 787 removed outlier: 3.663A pdb=" N GLN A 781 " --> pdb=" O GLY A 777 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N MET A 785 " --> pdb=" O GLN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 808 removed outlier: 3.660A pdb=" N ALA A 801 " --> pdb=" O HIS A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 830 Processing helix chain 'C' and resid 135 through 158 removed outlier: 3.747A pdb=" N ASN C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.671A pdb=" N ILE C 163 " --> pdb=" O LEU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 182 Processing helix chain 'C' and resid 184 through 206 Proline residue: C 197 - end of helix Processing helix chain 'C' and resid 206 through 218 Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'C' and resid 236 through 245 Processing helix chain 'C' and resid 251 through 261 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 301 through 311 removed outlier: 4.013A pdb=" N THR C 306 " --> pdb=" O HIS C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 344 No H-bonds generated for 'chain 'C' and resid 342 through 344' Processing helix chain 'C' and resid 374 through 391 removed outlier: 4.205A pdb=" N LEU C 378 " --> pdb=" O PRO C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 396 Processing helix chain 'C' and resid 412 through 419 Processing helix chain 'C' and resid 424 through 432 Processing helix chain 'C' and resid 446 through 450 Processing helix chain 'C' and resid 459 through 481 Processing helix chain 'C' and resid 525 through 530 removed outlier: 3.679A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 546 removed outlier: 4.155A pdb=" N ASP C 545 " --> pdb=" O ASP C 542 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER C 546 " --> pdb=" O LEU C 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 542 through 546' Processing helix chain 'C' and resid 549 through 554 removed outlier: 3.811A pdb=" N PHE C 553 " --> pdb=" O ILE C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 563 Processing helix chain 'C' and resid 563 through 568 Processing helix chain 'C' and resid 589 through 622 removed outlier: 3.881A pdb=" N LEU C 593 " --> pdb=" O GLY C 589 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N GLY C 595 " --> pdb=" O ARG C 591 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR C 597 " --> pdb=" O LEU C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 625 No H-bonds generated for 'chain 'C' and resid 623 through 625' Processing helix chain 'C' and resid 627 through 655 Processing helix chain 'C' and resid 657 through 667 Processing helix chain 'C' and resid 670 through 682 Processing helix chain 'C' and resid 683 through 688 removed outlier: 3.801A pdb=" N TYR C 686 " --> pdb=" O THR C 683 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS C 688 " --> pdb=" O ASP C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 703 Processing helix chain 'C' and resid 738 through 774 removed outlier: 3.741A pdb=" N GLU C 742 " --> pdb=" O LEU C 738 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN C 768 " --> pdb=" O LYS C 764 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE C 772 " --> pdb=" O GLN C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 780 through 794 removed outlier: 3.790A pdb=" N CYS C 784 " --> pdb=" O ASP C 780 " (cutoff:3.500A) Processing helix chain 'C' and resid 799 through 817 removed outlier: 3.842A pdb=" N LYS C 803 " --> pdb=" O CYS C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 824 No H-bonds generated for 'chain 'C' and resid 822 through 824' Processing helix chain 'C' and resid 825 through 848 removed outlier: 3.785A pdb=" N PHE C 829 " --> pdb=" O TYR C 825 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR C 848 " --> pdb=" O PHE C 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 20 Processing helix chain 'B' and resid 32 through 39 Processing helix chain 'B' and resid 45 through 55 removed outlier: 4.141A pdb=" N MET B 52 " --> pdb=" O GLU B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 77 Processing helix chain 'B' and resid 82 through 91 removed outlier: 3.767A pdb=" N ILE B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 110 Processing helix chain 'B' and resid 118 through 129 Processing helix chain 'B' and resid 139 through 144 Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 267 Processing sheet with id=AA2, first strand: chain 'A' and resid 468 through 469 removed outlier: 3.674A pdb=" N GLY A 474 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 767 through 768 removed outlier: 3.587A pdb=" N GLU A 839 " --> pdb=" O PHE A 893 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 767 through 768 removed outlier: 3.587A pdb=" N GLU A 839 " --> pdb=" O PHE A 893 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG A 890 " --> pdb=" O ASP A 881 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 850 through 852 removed outlier: 4.534A pdb=" N GLU A 862 " --> pdb=" O VAL A 852 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 105 through 109 Processing sheet with id=AA7, first strand: chain 'C' and resid 121 through 124 removed outlier: 8.366A pdb=" N ALA C 583 " --> pdb=" O SER C 128 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N SER C 585 " --> pdb=" O PRO C 130 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LYS C 132 " --> pdb=" O SER C 585 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR C 582 " --> pdb=" O ASP C 577 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 291 through 292 removed outlier: 3.516A pdb=" N ASN C 299 " --> pdb=" O PHE C 292 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 346 through 350 removed outlier: 4.654A pdb=" N ARG C 348 " --> pdb=" O LEU C 355 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LYS C 444 " --> pdb=" O PRO C 404 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 482 through 483 Processing sheet with id=AB2, first strand: chain 'C' and resid 535 through 536 Processing sheet with id=AB3, first strand: chain 'B' and resid 27 through 29 557 hydrogen bonds defined for protein. 1608 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.18 Time building geometry restraints manager: 4.64 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: 3528 1.34 - 1.46: 2247 1.46 - 1.58: 5128 1.58 - 1.70: 0 1.70 - 1.81: 65 Bond restraints: 10968 Sorted by residual: bond pdb=" CG1 ILE B 53 " pdb=" CD1 ILE B 53 " ideal model delta sigma weight residual 1.513 1.448 0.065 3.90e-02 6.57e+02 2.76e+00 bond pdb=" CG1 ILE C 610 " pdb=" CD1 ILE C 610 " ideal model delta sigma weight residual 1.513 1.458 0.055 3.90e-02 6.57e+02 1.95e+00 bond pdb=" CG LEU C 535 " pdb=" CD2 LEU C 535 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.45e+00 bond pdb=" C THR C 313 " pdb=" N GLU C 314 " ideal model delta sigma weight residual 1.331 1.306 0.025 2.07e-02 2.33e+03 1.42e+00 bond pdb=" CB TRP C 681 " pdb=" CG TRP C 681 " ideal model delta sigma weight residual 1.498 1.461 0.037 3.10e-02 1.04e+03 1.42e+00 ... (remaining 10963 not shown) Histogram of bond angle deviations from ideal: 98.99 - 105.99: 224 105.99 - 112.98: 5913 112.98 - 119.97: 3842 119.97 - 126.97: 4754 126.97 - 133.96: 103 Bond angle restraints: 14836 Sorted by residual: angle pdb=" N ILE A 525 " pdb=" CA ILE A 525 " pdb=" C ILE A 525 " ideal model delta sigma weight residual 113.53 110.53 3.00 9.80e-01 1.04e+00 9.40e+00 angle pdb=" CB MET B 73 " pdb=" CG MET B 73 " pdb=" SD MET B 73 " ideal model delta sigma weight residual 112.70 121.09 -8.39 3.00e+00 1.11e-01 7.81e+00 angle pdb=" C GLY A 542 " pdb=" N MET A 543 " pdb=" CA MET A 543 " ideal model delta sigma weight residual 121.31 125.34 -4.03 1.49e+00 4.50e-01 7.30e+00 angle pdb=" C ASP C 627 " pdb=" N LYS C 628 " pdb=" CA LYS C 628 " ideal model delta sigma weight residual 120.58 124.01 -3.43 1.32e+00 5.74e-01 6.73e+00 angle pdb=" CA GLY C 569 " pdb=" C GLY C 569 " pdb=" O GLY C 569 " ideal model delta sigma weight residual 122.59 120.04 2.55 1.04e+00 9.25e-01 6.00e+00 ... (remaining 14831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 6043 17.38 - 34.77: 482 34.77 - 52.15: 66 52.15 - 69.53: 17 69.53 - 86.91: 11 Dihedral angle restraints: 6619 sinusoidal: 2624 harmonic: 3995 Sorted by residual: dihedral pdb=" CA TYR C 702 " pdb=" C TYR C 702 " pdb=" N SER C 703 " pdb=" CA SER C 703 " ideal model delta harmonic sigma weight residual 180.00 159.96 20.04 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA ALA A 787 " pdb=" C ALA A 787 " pdb=" N ASN A 788 " pdb=" CA ASN A 788 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA LYS C 316 " pdb=" C LYS C 316 " pdb=" N GLU C 317 " pdb=" CA GLU C 317 " ideal model delta harmonic sigma weight residual 180.00 160.68 19.32 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 6616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1308 0.053 - 0.105: 309 0.105 - 0.158: 30 0.158 - 0.211: 2 0.211 - 0.263: 1 Chirality restraints: 1650 Sorted by residual: chirality pdb=" CA GLU A 295 " pdb=" N GLU A 295 " pdb=" C GLU A 295 " pdb=" CB GLU A 295 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB VAL A 334 " pdb=" CA VAL A 334 " pdb=" CG1 VAL A 334 " pdb=" CG2 VAL A 334 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA PHE C 475 " pdb=" N PHE C 475 " pdb=" C PHE C 475 " pdb=" CB PHE C 475 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.29e-01 ... (remaining 1647 not shown) Planarity restraints: 1919 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 432 " 0.020 2.00e-02 2.50e+03 1.89e-02 8.97e+00 pdb=" CG TRP A 432 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 432 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 432 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 432 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 432 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 432 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 432 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 432 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 432 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 628 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO C 629 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 629 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 629 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 581 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO A 582 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 582 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 582 " 0.025 5.00e-02 4.00e+02 ... (remaining 1916 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 217 2.67 - 3.22: 10874 3.22 - 3.78: 16950 3.78 - 4.34: 23028 4.34 - 4.90: 37389 Nonbonded interactions: 88458 Sorted by model distance: nonbonded pdb=" OG1 THR C 306 " pdb=" OG1 THR C 750 " model vdw 2.107 2.440 nonbonded pdb=" OH TYR C 326 " pdb=" OG SER C 546 " model vdw 2.124 2.440 nonbonded pdb=" OD1 ASP A 237 " pdb=" OG1 THR A 239 " model vdw 2.129 2.440 nonbonded pdb=" OG SER C 399 " pdb=" OD2 ASP C 473 " model vdw 2.147 2.440 nonbonded pdb=" OG SER C 220 " pdb=" OD1 ASP C 793 " model vdw 2.153 2.440 ... (remaining 88453 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 3.620 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: 7.240 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 31.190 Find NCS groups from input model: 0.310 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 : 0.006 0.065 10968 Z= 0.367 Angle : 0.676 8.386 14836 Z= 0.384 Chirality : 0.043 0.263 1650 Planarity : 0.004 0.045 1919 Dihedral : 13.131 86.914 4035 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.09 % Allowed : 0.35 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.23), residues: 1347 helix: 0.37 (0.19), residues: 720 sheet: -2.40 (0.51), residues: 95 loop : -1.89 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP A 432 HIS 0.007 0.001 HIS C 246 PHE 0.018 0.002 PHE C 475 TYR 0.018 0.002 TYR C 599 ARG 0.009 0.001 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 241 LEU cc_start: 0.9008 (tp) cc_final: 0.8780 (tp) REVERT: C 295 ARG cc_start: 0.6760 (ttm110) cc_final: 0.6463 (tpt-90) REVERT: C 353 THR cc_start: 0.8870 (m) cc_final: 0.8609 (p) REVERT: C 783 SER cc_start: 0.8881 (m) cc_final: 0.8629 (m) REVERT: B 73 MET cc_start: 0.8341 (mmm) cc_final: 0.7483 (mmm) outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.2403 time to fit residues: 54.2296 Evaluate side-chains 119 residues out of total 1211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 34 optimal weight: 0.1980 chunk 69 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 chunk 40 optimal weight: 0.0270 chunk 64 optimal weight: 2.9990 chunk 78 optimal weight: 0.2980 chunk 122 optimal weight: 0.0370 overall best weight: 0.2316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 HIS ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN C 180 ASN C 361 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10968 Z= 0.154 Angle : 0.518 8.735 14836 Z= 0.274 Chirality : 0.038 0.149 1650 Planarity : 0.004 0.045 1919 Dihedral : 4.264 21.329 1470 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.23 % Allowed : 6.22 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.24), residues: 1347 helix: 1.03 (0.20), residues: 730 sheet: -2.18 (0.52), residues: 93 loop : -1.57 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 549 HIS 0.006 0.001 HIS C 246 PHE 0.018 0.001 PHE C 475 TYR 0.014 0.001 TYR C 599 ARG 0.008 0.000 ARG C 676 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 156 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8360 (tp30) cc_final: 0.7916 (tp30) REVERT: C 295 ARG cc_start: 0.6662 (ttm110) cc_final: 0.6357 (tpt-90) REVERT: C 353 THR cc_start: 0.8769 (m) cc_final: 0.8523 (p) REVERT: C 480 GLU cc_start: 0.8173 (tp30) cc_final: 0.7568 (tp30) REVERT: C 696 MET cc_start: 0.7431 (mpp) cc_final: 0.7150 (mpp) REVERT: B 7 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7828 (tm-30) REVERT: B 17 PHE cc_start: 0.8811 (t80) cc_final: 0.8398 (t80) outliers start: 14 outliers final: 7 residues processed: 162 average time/residue: 0.2057 time to fit residues: 49.5332 Evaluate side-chains 132 residues out of total 1211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 125 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 797 HIS Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 692 ASP Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 108 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 HIS ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN C 180 ASN C 361 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10968 Z= 0.209 Angle : 0.508 7.198 14836 Z= 0.264 Chirality : 0.039 0.153 1650 Planarity : 0.004 0.044 1919 Dihedral : 4.118 18.883 1470 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.40 % Allowed : 8.94 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.24), residues: 1347 helix: 1.26 (0.20), residues: 729 sheet: -2.12 (0.50), residues: 97 loop : -1.46 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 210 HIS 0.005 0.001 HIS C 572 PHE 0.017 0.001 PHE B 20 TYR 0.012 0.001 TYR A 347 ARG 0.004 0.000 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 137 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8391 (tp30) cc_final: 0.8035 (tp30) REVERT: A 295 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7362 (mp0) REVERT: A 543 MET cc_start: 0.7598 (ppp) cc_final: 0.7391 (ppp) REVERT: A 785 MET cc_start: 0.8031 (tpp) cc_final: 0.7479 (tpt) REVERT: C 295 ARG cc_start: 0.6673 (ttm110) cc_final: 0.6365 (tpt-90) REVERT: C 353 THR cc_start: 0.8797 (m) cc_final: 0.8494 (p) REVERT: C 480 GLU cc_start: 0.8216 (tp30) cc_final: 0.7584 (tp30) REVERT: C 626 MET cc_start: 0.7100 (mpp) cc_final: 0.6816 (tpt) REVERT: C 756 MET cc_start: 0.7803 (mmt) cc_final: 0.7563 (mmm) REVERT: B 17 PHE cc_start: 0.8854 (t80) cc_final: 0.8382 (t80) outliers start: 16 outliers final: 12 residues processed: 149 average time/residue: 0.2198 time to fit residues: 48.1703 Evaluate side-chains 137 residues out of total 1211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 797 HIS Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 692 ASP Chi-restraints excluded: chain C residue 707 GLU Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain B residue 6 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 0.9990 chunk 92 optimal weight: 0.1980 chunk 63 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 64 optimal weight: 0.0570 chunk 116 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 GLN C 158 ASN C 180 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10968 Z= 0.166 Angle : 0.482 7.238 14836 Z= 0.251 Chirality : 0.038 0.151 1650 Planarity : 0.003 0.043 1919 Dihedral : 3.951 18.873 1470 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.75 % Allowed : 10.87 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.24), residues: 1347 helix: 1.49 (0.20), residues: 723 sheet: -1.96 (0.51), residues: 95 loop : -1.33 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 549 HIS 0.004 0.001 HIS C 171 PHE 0.015 0.001 PHE C 475 TYR 0.018 0.001 TYR A 256 ARG 0.004 0.000 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8412 (tp30) cc_final: 0.7998 (tp30) REVERT: A 295 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: A 408 MET cc_start: 0.7816 (tpp) cc_final: 0.7566 (mmm) REVERT: A 543 MET cc_start: 0.7634 (ppp) cc_final: 0.7393 (ppp) REVERT: A 785 MET cc_start: 0.8156 (tpp) cc_final: 0.7603 (tpt) REVERT: C 210 TRP cc_start: 0.8591 (t-100) cc_final: 0.8298 (t-100) REVERT: C 295 ARG cc_start: 0.6609 (ttm110) cc_final: 0.6329 (tpt-90) REVERT: C 480 GLU cc_start: 0.8221 (tp30) cc_final: 0.7525 (tp30) REVERT: C 626 MET cc_start: 0.7021 (mpp) cc_final: 0.6778 (tpt) REVERT: C 836 ASN cc_start: 0.8475 (t0) cc_final: 0.8244 (t0) REVERT: B 7 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7714 (tm-30) REVERT: B 17 PHE cc_start: 0.8814 (t80) cc_final: 0.8420 (t80) outliers start: 20 outliers final: 14 residues processed: 160 average time/residue: 0.2038 time to fit residues: 48.5030 Evaluate side-chains 142 residues out of total 1211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 797 HIS Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 692 ASP Chi-restraints excluded: chain C residue 696 MET Chi-restraints excluded: chain C residue 707 GLU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 10 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 2.9990 chunk 74 optimal weight: 0.0170 chunk 1 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 90 optimal weight: 0.0270 chunk 0 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 117 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN C 259 GLN C 611 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10968 Z= 0.148 Angle : 0.480 7.251 14836 Z= 0.247 Chirality : 0.037 0.153 1650 Planarity : 0.004 0.045 1919 Dihedral : 3.800 17.837 1470 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.19 % Allowed : 11.04 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.24), residues: 1347 helix: 1.64 (0.20), residues: 725 sheet: -1.66 (0.51), residues: 100 loop : -1.23 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 549 HIS 0.004 0.001 HIS C 171 PHE 0.022 0.001 PHE C 356 TYR 0.013 0.001 TYR A 347 ARG 0.010 0.000 ARG C 676 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8420 (tp30) cc_final: 0.7890 (tp30) REVERT: A 408 MET cc_start: 0.7834 (tpp) cc_final: 0.7621 (mmm) REVERT: C 210 TRP cc_start: 0.8582 (t-100) cc_final: 0.8319 (t-100) REVERT: C 295 ARG cc_start: 0.6493 (ttm110) cc_final: 0.6211 (tpt-90) REVERT: C 480 GLU cc_start: 0.8150 (tp30) cc_final: 0.7501 (tp30) REVERT: C 626 MET cc_start: 0.6978 (mpp) cc_final: 0.6733 (tpt) REVERT: C 756 MET cc_start: 0.7852 (mmt) cc_final: 0.7607 (mmm) REVERT: C 836 ASN cc_start: 0.8462 (t0) cc_final: 0.8240 (t0) REVERT: B 7 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7642 (tm-30) REVERT: B 17 PHE cc_start: 0.8748 (t80) cc_final: 0.8404 (t80) REVERT: B 33 LEU cc_start: 0.8233 (tp) cc_final: 0.7862 (tp) outliers start: 25 outliers final: 16 residues processed: 153 average time/residue: 0.2068 time to fit residues: 47.2586 Evaluate side-chains 139 residues out of total 1211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 797 HIS Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 692 ASP Chi-restraints excluded: chain C residue 707 GLU Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 40 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 130 optimal weight: 20.0000 chunk 108 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 10 optimal weight: 0.0370 chunk 68 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.6862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN C 611 GLN B 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10968 Z= 0.183 Angle : 0.486 7.262 14836 Z= 0.251 Chirality : 0.038 0.168 1650 Planarity : 0.003 0.040 1919 Dihedral : 3.782 16.875 1470 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.02 % Allowed : 12.36 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.24), residues: 1347 helix: 1.72 (0.20), residues: 723 sheet: -1.38 (0.52), residues: 97 loop : -1.28 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 549 HIS 0.004 0.001 HIS C 572 PHE 0.014 0.001 PHE B 20 TYR 0.016 0.001 TYR C 606 ARG 0.008 0.000 ARG C 676 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 133 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8419 (tp30) cc_final: 0.8065 (tp30) REVERT: A 408 MET cc_start: 0.7926 (tpp) cc_final: 0.7712 (mmm) REVERT: A 785 MET cc_start: 0.7994 (tpp) cc_final: 0.7481 (tpt) REVERT: C 210 TRP cc_start: 0.8637 (t-100) cc_final: 0.8393 (t-100) REVERT: C 295 ARG cc_start: 0.6533 (ttm110) cc_final: 0.6242 (tpt-90) REVERT: C 480 GLU cc_start: 0.8229 (tp30) cc_final: 0.7530 (tp30) REVERT: C 576 PHE cc_start: 0.8229 (t80) cc_final: 0.7966 (t80) REVERT: C 626 MET cc_start: 0.7033 (mpp) cc_final: 0.6758 (tpt) REVERT: C 836 ASN cc_start: 0.8506 (t0) cc_final: 0.8241 (t0) REVERT: B 7 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7668 (tm-30) REVERT: B 17 PHE cc_start: 0.8777 (t80) cc_final: 0.8403 (t80) REVERT: B 33 LEU cc_start: 0.8260 (tp) cc_final: 0.7932 (tp) REVERT: B 52 MET cc_start: 0.7685 (tpp) cc_final: 0.7311 (tpp) outliers start: 23 outliers final: 17 residues processed: 146 average time/residue: 0.2374 time to fit residues: 51.7832 Evaluate side-chains 139 residues out of total 1211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 797 HIS Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 692 ASP Chi-restraints excluded: chain C residue 696 MET Chi-restraints excluded: chain C residue 707 GLU Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 40 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 chunk 81 optimal weight: 8.9990 chunk 79 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 80 optimal weight: 0.0370 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 611 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10968 Z= 0.216 Angle : 0.518 7.626 14836 Z= 0.265 Chirality : 0.039 0.155 1650 Planarity : 0.004 0.049 1919 Dihedral : 3.853 18.759 1470 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.28 % Allowed : 12.88 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.24), residues: 1347 helix: 1.72 (0.20), residues: 725 sheet: -1.30 (0.53), residues: 95 loop : -1.27 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 549 HIS 0.004 0.001 HIS C 572 PHE 0.015 0.001 PHE B 20 TYR 0.021 0.001 TYR A 246 ARG 0.007 0.000 ARG C 676 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8434 (tp30) cc_final: 0.8139 (tp30) REVERT: A 408 MET cc_start: 0.7992 (tpp) cc_final: 0.7792 (mmm) REVERT: A 543 MET cc_start: 0.7979 (ppp) cc_final: 0.7724 (ppp) REVERT: A 785 MET cc_start: 0.8092 (tpp) cc_final: 0.7582 (tpt) REVERT: C 295 ARG cc_start: 0.6697 (ttm110) cc_final: 0.6451 (tpt-90) REVERT: C 480 GLU cc_start: 0.8213 (tp30) cc_final: 0.7487 (tp30) REVERT: C 626 MET cc_start: 0.7078 (mpp) cc_final: 0.6820 (tpt) REVERT: C 836 ASN cc_start: 0.8532 (t0) cc_final: 0.8265 (t0) REVERT: B 7 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7698 (tm-30) REVERT: B 17 PHE cc_start: 0.8831 (t80) cc_final: 0.8442 (t80) REVERT: B 33 LEU cc_start: 0.8402 (tp) cc_final: 0.8167 (tp) outliers start: 26 outliers final: 21 residues processed: 151 average time/residue: 0.2199 time to fit residues: 49.1523 Evaluate side-chains 144 residues out of total 1211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 797 HIS Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 692 ASP Chi-restraints excluded: chain C residue 696 MET Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 707 GLU Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 40 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 102 optimal weight: 0.5980 chunk 118 optimal weight: 0.3980 chunk 124 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN C 611 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10968 Z= 0.198 Angle : 0.506 8.607 14836 Z= 0.260 Chirality : 0.039 0.165 1650 Planarity : 0.004 0.049 1919 Dihedral : 3.853 16.889 1470 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.19 % Allowed : 13.67 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.24), residues: 1347 helix: 1.71 (0.20), residues: 725 sheet: -1.24 (0.53), residues: 95 loop : -1.26 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 549 HIS 0.004 0.001 HIS C 572 PHE 0.020 0.001 PHE A 501 TYR 0.024 0.002 TYR A 246 ARG 0.007 0.000 ARG C 676 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8428 (tp30) cc_final: 0.8126 (tp30) REVERT: A 785 MET cc_start: 0.8111 (tpp) cc_final: 0.7589 (tpt) REVERT: C 295 ARG cc_start: 0.6718 (ttm110) cc_final: 0.6456 (tpt-90) REVERT: C 480 GLU cc_start: 0.8205 (tp30) cc_final: 0.7467 (tp30) REVERT: C 626 MET cc_start: 0.7006 (mpp) cc_final: 0.6661 (tpt) REVERT: C 836 ASN cc_start: 0.8518 (t0) cc_final: 0.8252 (t0) REVERT: B 7 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7728 (tm-30) REVERT: B 17 PHE cc_start: 0.8836 (t80) cc_final: 0.8439 (t80) REVERT: B 33 LEU cc_start: 0.8341 (tp) cc_final: 0.8030 (tp) outliers start: 25 outliers final: 23 residues processed: 145 average time/residue: 0.2049 time to fit residues: 43.7974 Evaluate side-chains 145 residues out of total 1211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 797 HIS Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 692 ASP Chi-restraints excluded: chain C residue 696 MET Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 707 GLU Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 40 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.5980 chunk 121 optimal weight: 0.6980 chunk 124 optimal weight: 0.0470 chunk 72 optimal weight: 6.9990 chunk 52 optimal weight: 0.2980 chunk 95 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 120 optimal weight: 0.0070 chunk 79 optimal weight: 0.8980 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN C 611 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10968 Z= 0.144 Angle : 0.511 10.304 14836 Z= 0.259 Chirality : 0.038 0.176 1650 Planarity : 0.003 0.040 1919 Dihedral : 3.784 17.955 1470 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.28 % Allowed : 13.76 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.24), residues: 1347 helix: 1.88 (0.20), residues: 719 sheet: -1.18 (0.53), residues: 100 loop : -1.23 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 432 HIS 0.004 0.001 HIS C 171 PHE 0.019 0.001 PHE C 174 TYR 0.020 0.001 TYR C 597 ARG 0.007 0.000 ARG C 676 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8405 (tp30) cc_final: 0.8034 (tp30) REVERT: A 785 MET cc_start: 0.8093 (tpp) cc_final: 0.7564 (tpt) REVERT: C 210 TRP cc_start: 0.8643 (t-100) cc_final: 0.8376 (t-100) REVERT: C 295 ARG cc_start: 0.6658 (ttm110) cc_final: 0.6402 (tpt-90) REVERT: C 480 GLU cc_start: 0.8130 (tp30) cc_final: 0.7418 (tp30) REVERT: C 626 MET cc_start: 0.6907 (mpp) cc_final: 0.6578 (tpt) REVERT: C 756 MET cc_start: 0.7779 (mmt) cc_final: 0.7576 (mmm) REVERT: C 836 ASN cc_start: 0.8446 (t0) cc_final: 0.8218 (t0) REVERT: B 7 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7665 (tm-30) REVERT: B 17 PHE cc_start: 0.8774 (t80) cc_final: 0.8449 (t80) REVERT: B 33 LEU cc_start: 0.8190 (tp) cc_final: 0.7730 (tp) outliers start: 26 outliers final: 22 residues processed: 147 average time/residue: 0.2206 time to fit residues: 47.7440 Evaluate side-chains 140 residues out of total 1211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 797 HIS Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 692 ASP Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 707 GLU Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 40 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 0.1980 chunk 78 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 134 optimal weight: 30.0000 chunk 123 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 ASN C 383 GLN C 611 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10968 Z= 0.181 Angle : 0.499 7.565 14836 Z= 0.256 Chirality : 0.038 0.166 1650 Planarity : 0.003 0.039 1919 Dihedral : 3.804 17.615 1470 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.19 % Allowed : 13.85 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.24), residues: 1347 helix: 1.88 (0.20), residues: 720 sheet: -1.06 (0.55), residues: 95 loop : -1.26 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 432 HIS 0.004 0.001 HIS C 572 PHE 0.020 0.001 PHE A 501 TYR 0.027 0.001 TYR A 246 ARG 0.006 0.000 ARG C 676 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 127 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.8424 (tp30) cc_final: 0.8105 (tp30) REVERT: C 210 TRP cc_start: 0.8675 (t-100) cc_final: 0.8394 (t-100) REVERT: C 295 ARG cc_start: 0.6712 (ttm110) cc_final: 0.6465 (tpt-90) REVERT: C 480 GLU cc_start: 0.8159 (tp30) cc_final: 0.7449 (tp30) REVERT: C 626 MET cc_start: 0.7059 (mpp) cc_final: 0.6676 (tpt) REVERT: C 756 MET cc_start: 0.7842 (mmt) cc_final: 0.7626 (mmm) REVERT: C 836 ASN cc_start: 0.8483 (t0) cc_final: 0.8229 (t0) REVERT: B 7 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7686 (tm-30) REVERT: B 17 PHE cc_start: 0.8769 (t80) cc_final: 0.8447 (t80) REVERT: B 33 LEU cc_start: 0.8143 (tp) cc_final: 0.7684 (tp) outliers start: 25 outliers final: 22 residues processed: 144 average time/residue: 0.2086 time to fit residues: 44.0701 Evaluate side-chains 144 residues out of total 1211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 122 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 797 HIS Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 692 ASP Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 707 GLU Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 40 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 15 optimal weight: 0.0870 chunk 29 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 611 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.130197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.101167 restraints weight = 18884.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.101669 restraints weight = 15760.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.102438 restraints weight = 12886.340| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10968 Z= 0.198 Angle : 0.532 9.212 14836 Z= 0.268 Chirality : 0.039 0.162 1650 Planarity : 0.003 0.039 1919 Dihedral : 3.835 17.359 1470 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.19 % Allowed : 14.11 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.24), residues: 1347 helix: 1.86 (0.20), residues: 720 sheet: -1.11 (0.53), residues: 100 loop : -1.23 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 432 HIS 0.004 0.001 HIS C 572 PHE 0.012 0.001 PHE C 174 TYR 0.031 0.002 TYR A 246 ARG 0.006 0.000 ARG C 676 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2200.75 seconds wall clock time: 41 minutes 3.88 seconds (2463.88 seconds total)