Starting phenix.real_space_refine on Thu Mar 14 23:04:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r7y_4747/03_2024/6r7y_4747.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r7y_4747/03_2024/6r7y_4747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r7y_4747/03_2024/6r7y_4747.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r7y_4747/03_2024/6r7y_4747.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r7y_4747/03_2024/6r7y_4747.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r7y_4747/03_2024/6r7y_4747.pdb" } resolution = 4.2 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 54 5.16 5 C 6640 2.51 5 N 1618 2.21 5 O 1744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 285": "NH1" <-> "NH2" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10062 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 5028 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 23, 'TRANS': 603} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "B" Number of atoms: 5028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 5028 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 23, 'TRANS': 603} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.63, per 1000 atoms: 0.56 Number of scatterers: 10062 At special positions: 0 Unit cell: (84.666, 132.342, 98.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 54 16.00 O 1744 8.00 N 1618 7.00 C 6640 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: 4.02 Conformation dependent library (CDL) restraints added in 1.8 seconds 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 6 sheets defined 67.6% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 28 through 41 removed outlier: 3.746A pdb=" N ALA A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 67 removed outlier: 3.639A pdb=" N GLN A 67 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 87 Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.854A pdb=" N PHE A 108 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 134 Processing helix chain 'A' and resid 156 through 164 removed outlier: 3.563A pdb=" N ARG A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 196 through 205 Processing helix chain 'A' and resid 206 through 220 removed outlier: 3.545A pdb=" N PHE A 220 " --> pdb=" O GLU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 236 through 240 removed outlier: 4.178A pdb=" N ASP A 239 " --> pdb=" O VAL A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 273 removed outlier: 3.810A pdb=" N ALA A 247 " --> pdb=" O TYR A 243 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 316 removed outlier: 3.643A pdb=" N ARG A 310 " --> pdb=" O PRO A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 350 Processing helix chain 'A' and resid 352 through 355 removed outlier: 3.721A pdb=" N THR A 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 355' Processing helix chain 'A' and resid 356 through 387 removed outlier: 3.907A pdb=" N TYR A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Proline residue: A 362 - end of helix removed outlier: 3.924A pdb=" N ARG A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 422 removed outlier: 3.696A pdb=" N TYR A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N SER A 415 " --> pdb=" O ASN A 411 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU A 416 " --> pdb=" O CYS A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 449 removed outlier: 3.636A pdb=" N SER A 449 " --> pdb=" O GLN A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 469 removed outlier: 3.760A pdb=" N ALA A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 removed outlier: 3.673A pdb=" N TYR A 479 " --> pdb=" O ASP A 475 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLN A 481 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU A 487 " --> pdb=" O ILE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 510 removed outlier: 4.020A pdb=" N LEU A 501 " --> pdb=" O ASP A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 539 removed outlier: 3.825A pdb=" N ASN A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASN A 531 " --> pdb=" O PHE A 527 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 534 " --> pdb=" O VAL A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 575 removed outlier: 3.906A pdb=" N VAL A 567 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 568 " --> pdb=" O VAL A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 613 removed outlier: 3.941A pdb=" N LEU A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 640 Processing helix chain 'B' and resid 28 through 41 removed outlier: 3.746A pdb=" N ALA B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 67 removed outlier: 3.639A pdb=" N GLN B 67 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 87 Processing helix chain 'B' and resid 104 through 108 removed outlier: 3.854A pdb=" N PHE B 108 " --> pdb=" O ARG B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 134 Processing helix chain 'B' and resid 156 through 164 removed outlier: 3.563A pdb=" N ARG B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 196 through 205 Processing helix chain 'B' and resid 206 through 220 removed outlier: 3.546A pdb=" N PHE B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 230 through 235 Processing helix chain 'B' and resid 236 through 240 removed outlier: 4.177A pdb=" N ASP B 239 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 273 removed outlier: 3.810A pdb=" N ALA B 247 " --> pdb=" O TYR B 243 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 316 removed outlier: 3.643A pdb=" N ARG B 310 " --> pdb=" O PRO B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 350 Processing helix chain 'B' and resid 352 through 355 removed outlier: 3.722A pdb=" N THR B 355 " --> pdb=" O SER B 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 355' Processing helix chain 'B' and resid 356 through 387 removed outlier: 3.908A pdb=" N TYR B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Proline residue: B 362 - end of helix removed outlier: 3.924A pdb=" N ARG B 375 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 422 removed outlier: 3.696A pdb=" N TYR B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N SER B 415 " --> pdb=" O ASN B 411 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU B 416 " --> pdb=" O CYS B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 449 removed outlier: 3.636A pdb=" N SER B 449 " --> pdb=" O GLN B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 469 removed outlier: 3.762A pdb=" N ALA B 469 " --> pdb=" O ARG B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 487 removed outlier: 3.674A pdb=" N TYR B 479 " --> pdb=" O ASP B 475 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLN B 481 " --> pdb=" O THR B 477 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU B 487 " --> pdb=" O ILE B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 510 removed outlier: 4.019A pdb=" N LEU B 501 " --> pdb=" O ASP B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 539 removed outlier: 3.825A pdb=" N ASN B 525 " --> pdb=" O PHE B 521 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR B 528 " --> pdb=" O LEU B 524 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASN B 531 " --> pdb=" O PHE B 527 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 534 " --> pdb=" O VAL B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 575 removed outlier: 3.906A pdb=" N VAL B 567 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL B 568 " --> pdb=" O VAL B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 613 removed outlier: 3.940A pdb=" N LEU B 593 " --> pdb=" O ALA B 589 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 640 Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.734A pdb=" N GLN A 169 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 91 Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 294 Processing sheet with id=AA4, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.734A pdb=" N GLN B 169 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 89 through 91 Processing sheet with id=AA6, first strand: chain 'B' and resid 291 through 294 614 hydrogen bonds defined for protein. 1806 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: 2.95 Time building geometry restraints manager: 4.30 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: 3073 1.34 - 1.45: 1893 1.45 - 1.57: 5256 1.57 - 1.69: 0 1.69 - 1.80: 90 Bond restraints: 10312 Sorted by residual: bond pdb=" CB PHE B 218 " pdb=" CG PHE B 218 " ideal model delta sigma weight residual 1.502 1.457 0.045 2.30e-02 1.89e+03 3.74e+00 bond pdb=" CB PHE A 218 " pdb=" CG PHE A 218 " ideal model delta sigma weight residual 1.502 1.458 0.044 2.30e-02 1.89e+03 3.74e+00 bond pdb=" CG GLN B 556 " pdb=" CD GLN B 556 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.56e+00 bond pdb=" CB GLN A 556 " pdb=" CG GLN A 556 " ideal model delta sigma weight residual 1.520 1.464 0.056 3.00e-02 1.11e+03 3.46e+00 bond pdb=" CG GLN A 556 " pdb=" CD GLN A 556 " ideal model delta sigma weight residual 1.516 1.470 0.046 2.50e-02 1.60e+03 3.41e+00 ... (remaining 10307 not shown) Histogram of bond angle deviations from ideal: 98.92 - 105.96: 200 105.96 - 113.01: 5536 113.01 - 120.06: 4097 120.06 - 127.10: 4063 127.10 - 134.15: 112 Bond angle restraints: 14008 Sorted by residual: angle pdb=" N SER A 352 " pdb=" CA SER A 352 " pdb=" C SER A 352 " ideal model delta sigma weight residual 113.43 106.65 6.78 1.26e+00 6.30e-01 2.90e+01 angle pdb=" N SER B 352 " pdb=" CA SER B 352 " pdb=" C SER B 352 " ideal model delta sigma weight residual 113.43 106.67 6.76 1.26e+00 6.30e-01 2.88e+01 angle pdb=" CA VAL B 236 " pdb=" CB VAL B 236 " pdb=" CG1 VAL B 236 " ideal model delta sigma weight residual 110.40 116.68 -6.28 1.70e+00 3.46e-01 1.37e+01 angle pdb=" CA VAL A 236 " pdb=" CB VAL A 236 " pdb=" CG1 VAL A 236 " ideal model delta sigma weight residual 110.40 116.67 -6.27 1.70e+00 3.46e-01 1.36e+01 angle pdb=" N SER A 350 " pdb=" CA SER A 350 " pdb=" C SER A 350 " ideal model delta sigma weight residual 111.24 115.96 -4.72 1.29e+00 6.01e-01 1.34e+01 ... (remaining 14003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 5356 16.01 - 32.02: 602 32.02 - 48.04: 104 48.04 - 64.05: 22 64.05 - 80.06: 4 Dihedral angle restraints: 6088 sinusoidal: 2370 harmonic: 3718 Sorted by residual: dihedral pdb=" CA ASN A 349 " pdb=" C ASN A 349 " pdb=" N SER A 350 " pdb=" CA SER A 350 " ideal model delta harmonic sigma weight residual -180.00 -157.57 -22.43 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA ASN B 349 " pdb=" C ASN B 349 " pdb=" N SER B 350 " pdb=" CA SER B 350 " ideal model delta harmonic sigma weight residual 180.00 -157.58 -22.42 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" C VAL A 236 " pdb=" N VAL A 236 " pdb=" CA VAL A 236 " pdb=" CB VAL A 236 " ideal model delta harmonic sigma weight residual -122.00 -130.39 8.39 0 2.50e+00 1.60e-01 1.13e+01 ... (remaining 6085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 918 0.048 - 0.096: 486 0.096 - 0.144: 155 0.144 - 0.192: 25 0.192 - 0.240: 4 Chirality restraints: 1588 Sorted by residual: chirality pdb=" CB VAL B 236 " pdb=" CA VAL B 236 " pdb=" CG1 VAL B 236 " pdb=" CG2 VAL B 236 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CB VAL A 236 " pdb=" CA VAL A 236 " pdb=" CG1 VAL A 236 " pdb=" CG2 VAL A 236 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA HIS A 399 " pdb=" N HIS A 399 " pdb=" C HIS A 399 " pdb=" CB HIS A 399 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1585 not shown) Planarity restraints: 1742 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 337 " -0.026 2.00e-02 2.50e+03 2.03e-02 7.19e+00 pdb=" CG PHE B 337 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE B 337 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B 337 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 337 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 337 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 337 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 337 " 0.026 2.00e-02 2.50e+03 2.02e-02 7.11e+00 pdb=" CG PHE A 337 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 337 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 337 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 337 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 337 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 337 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 355 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" C THR B 355 " 0.044 2.00e-02 2.50e+03 pdb=" O THR B 355 " -0.017 2.00e-02 2.50e+03 pdb=" N SER B 356 " -0.015 2.00e-02 2.50e+03 ... (remaining 1739 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1077 2.73 - 3.27: 9444 3.27 - 3.82: 16186 3.82 - 4.36: 18685 4.36 - 4.90: 32430 Nonbonded interactions: 77822 Sorted by model distance: nonbonded pdb=" OE2 GLU A 500 " pdb="CA CA A 701 " model vdw 2.188 2.510 nonbonded pdb=" OE2 GLU B 500 " pdb="CA CA B 701 " model vdw 2.188 2.510 nonbonded pdb=" OE2 GLU A 448 " pdb="CA CA A 702 " model vdw 2.233 2.510 nonbonded pdb=" OE2 GLU B 448 " pdb="CA CA B 702 " model vdw 2.234 2.510 nonbonded pdb=" N ASN B 57 " pdb=" OD1 ASN B 57 " model vdw 2.297 2.520 ... (remaining 77817 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.120 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 29.830 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 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 : 0.010 0.073 10312 Z= 0.656 Angle : 1.069 9.070 14008 Z= 0.597 Chirality : 0.061 0.240 1588 Planarity : 0.007 0.056 1742 Dihedral : 13.583 80.059 3688 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.56 % Favored : 97.28 % Rotamer: Outliers : 1.71 % Allowed : 4.29 % Favored : 94.00 % 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: -3.14 (0.18), residues: 1250 helix: -2.09 (0.13), residues: 758 sheet: -0.85 (0.67), residues: 44 loop : -1.88 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 186 HIS 0.013 0.003 HIS B 399 PHE 0.046 0.004 PHE B 337 TYR 0.020 0.003 TYR B 243 ARG 0.004 0.001 ARG B 543 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 312 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.7666 (tt0) cc_final: 0.7377 (tt0) REVERT: A 70 TYR cc_start: 0.7259 (m-80) cc_final: 0.6987 (m-80) REVERT: A 125 GLN cc_start: 0.9075 (mt0) cc_final: 0.8811 (mt0) REVERT: A 158 LEU cc_start: 0.9190 (tp) cc_final: 0.8984 (tp) REVERT: A 176 SER cc_start: 0.8699 (p) cc_final: 0.8320 (t) REVERT: A 236 VAL cc_start: 0.9089 (p) cc_final: 0.8156 (m) REVERT: A 308 TYR cc_start: 0.8504 (p90) cc_final: 0.8089 (p90) REVERT: A 334 MET cc_start: 0.7969 (mmm) cc_final: 0.7548 (mmt) REVERT: A 370 ILE cc_start: 0.9353 (mt) cc_final: 0.9138 (pt) REVERT: A 459 HIS cc_start: 0.8586 (t70) cc_final: 0.8326 (t70) REVERT: A 514 VAL cc_start: 0.9060 (m) cc_final: 0.8804 (p) REVERT: A 531 ASN cc_start: 0.8825 (m-40) cc_final: 0.8321 (t0) REVERT: A 576 MET cc_start: 0.7967 (mtt) cc_final: 0.7652 (mtp) REVERT: A 599 GLU cc_start: 0.9113 (tm-30) cc_final: 0.8905 (tm-30) REVERT: A 611 PHE cc_start: 0.8353 (t80) cc_final: 0.8081 (t80) REVERT: A 627 LEU cc_start: 0.8933 (tp) cc_final: 0.8676 (tt) REVERT: B 22 GLU cc_start: 0.7636 (tt0) cc_final: 0.7395 (tt0) REVERT: B 40 ILE cc_start: 0.7943 (mt) cc_final: 0.7500 (mt) REVERT: B 81 LEU cc_start: 0.8636 (mt) cc_final: 0.8084 (tp) REVERT: B 125 GLN cc_start: 0.9165 (mt0) cc_final: 0.8745 (mt0) REVERT: B 176 SER cc_start: 0.8623 (p) cc_final: 0.8397 (t) REVERT: B 183 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7746 (mt-10) REVERT: B 270 TYR cc_start: 0.9063 (t80) cc_final: 0.8672 (t80) REVERT: B 334 MET cc_start: 0.7929 (mmm) cc_final: 0.7674 (mmt) REVERT: B 373 MET cc_start: 0.8512 (ttp) cc_final: 0.7786 (tpp) REVERT: B 431 GLN cc_start: 0.7993 (mt0) cc_final: 0.7790 (tm-30) REVERT: B 453 TYR cc_start: 0.9147 (t80) cc_final: 0.8806 (t80) REVERT: B 454 TRP cc_start: 0.8996 (t60) cc_final: 0.8551 (t-100) REVERT: B 504 GLN cc_start: 0.8449 (mt0) cc_final: 0.8222 (mm110) REVERT: B 531 ASN cc_start: 0.8866 (m-40) cc_final: 0.8243 (t0) REVERT: B 576 MET cc_start: 0.7916 (mtt) cc_final: 0.7613 (mtp) outliers start: 18 outliers final: 8 residues processed: 329 average time/residue: 0.2251 time to fit residues: 101.9684 Evaluate side-chains 193 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 185 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 112 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 HIS ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 ASN ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN B 525 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10312 Z= 0.192 Angle : 0.546 5.720 14008 Z= 0.284 Chirality : 0.038 0.142 1588 Planarity : 0.004 0.042 1742 Dihedral : 4.264 21.567 1370 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.64 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.22), residues: 1250 helix: 0.19 (0.17), residues: 782 sheet: -0.19 (0.72), residues: 44 loop : -1.46 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 186 HIS 0.005 0.001 HIS B 459 PHE 0.027 0.002 PHE B 407 TYR 0.017 0.001 TYR B 203 ARG 0.005 0.001 ARG B 539 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: A 81 LEU cc_start: 0.8595 (mt) cc_final: 0.8123 (tp) REVERT: A 91 GLU cc_start: 0.8006 (pm20) cc_final: 0.7645 (pm20) REVERT: A 121 MET cc_start: 0.7695 (tpp) cc_final: 0.7341 (tpp) REVERT: A 125 GLN cc_start: 0.8734 (mt0) cc_final: 0.8496 (mt0) REVERT: A 176 SER cc_start: 0.8570 (p) cc_final: 0.8263 (t) REVERT: A 217 TYR cc_start: 0.8940 (t80) cc_final: 0.8702 (t80) REVERT: A 373 MET cc_start: 0.8252 (ttp) cc_final: 0.7507 (tpp) REVERT: A 377 TYR cc_start: 0.8823 (t80) cc_final: 0.8524 (t80) REVERT: A 459 HIS cc_start: 0.8329 (t70) cc_final: 0.8117 (t70) REVERT: A 514 VAL cc_start: 0.9038 (m) cc_final: 0.8729 (p) REVERT: A 521 PHE cc_start: 0.8742 (m-10) cc_final: 0.8498 (m-10) REVERT: A 528 THR cc_start: 0.9293 (p) cc_final: 0.8896 (t) REVERT: A 540 VAL cc_start: 0.9206 (t) cc_final: 0.8820 (t) REVERT: A 576 MET cc_start: 0.7960 (mtt) cc_final: 0.7743 (mtp) REVERT: B 81 LEU cc_start: 0.8727 (mt) cc_final: 0.8223 (tp) REVERT: B 176 SER cc_start: 0.8573 (p) cc_final: 0.8113 (t) REVERT: B 187 TYR cc_start: 0.7779 (m-10) cc_final: 0.6941 (m-10) REVERT: B 217 TYR cc_start: 0.8675 (t80) cc_final: 0.8346 (t80) REVERT: B 327 TYR cc_start: 0.7774 (t80) cc_final: 0.7483 (t80) REVERT: B 373 MET cc_start: 0.8365 (ttp) cc_final: 0.7852 (tpp) REVERT: B 453 TYR cc_start: 0.8953 (t80) cc_final: 0.8572 (t80) REVERT: B 458 LYS cc_start: 0.8326 (mttt) cc_final: 0.8112 (mttp) REVERT: B 504 GLN cc_start: 0.8087 (mt0) cc_final: 0.7877 (tt0) REVERT: B 531 ASN cc_start: 0.8558 (m-40) cc_final: 0.7753 (t0) REVERT: B 576 MET cc_start: 0.7988 (mtt) cc_final: 0.7767 (mtp) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.1786 time to fit residues: 70.0922 Evaluate side-chains 174 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 111 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 90 optimal weight: 20.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 GLN A 525 ASN B 250 ASN ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10312 Z= 0.272 Angle : 0.597 8.090 14008 Z= 0.301 Chirality : 0.040 0.136 1588 Planarity : 0.004 0.039 1742 Dihedral : 4.139 21.045 1370 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.48 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % 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: 0.47 (0.23), residues: 1250 helix: 1.01 (0.18), residues: 782 sheet: 0.01 (0.74), residues: 44 loop : -0.89 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 261 HIS 0.005 0.001 HIS B 459 PHE 0.023 0.002 PHE A 611 TYR 0.030 0.002 TYR A 187 ARG 0.005 0.001 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.8665 (mt) cc_final: 0.8274 (tp) REVERT: A 91 GLU cc_start: 0.8204 (pm20) cc_final: 0.7886 (pm20) REVERT: A 117 ASP cc_start: 0.8120 (m-30) cc_final: 0.7835 (t70) REVERT: A 121 MET cc_start: 0.8011 (tpp) cc_final: 0.7740 (tpp) REVERT: A 125 GLN cc_start: 0.8859 (mt0) cc_final: 0.8618 (mt0) REVERT: A 217 TYR cc_start: 0.8902 (t80) cc_final: 0.8635 (t80) REVERT: A 373 MET cc_start: 0.8249 (ttp) cc_final: 0.7516 (tpp) REVERT: A 377 TYR cc_start: 0.9160 (t80) cc_final: 0.8922 (t80) REVERT: A 405 LEU cc_start: 0.9393 (tp) cc_final: 0.9100 (tp) REVERT: A 459 HIS cc_start: 0.8252 (t70) cc_final: 0.8021 (t70) REVERT: A 528 THR cc_start: 0.9349 (p) cc_final: 0.8977 (t) REVERT: A 576 MET cc_start: 0.8132 (mtt) cc_final: 0.7866 (mtp) REVERT: B 81 LEU cc_start: 0.8778 (mt) cc_final: 0.8302 (tp) REVERT: B 176 SER cc_start: 0.8633 (p) cc_final: 0.8154 (t) REVERT: B 217 TYR cc_start: 0.8696 (t80) cc_final: 0.8400 (t80) REVERT: B 373 MET cc_start: 0.8407 (ttp) cc_final: 0.7839 (tpp) REVERT: B 405 LEU cc_start: 0.9418 (tp) cc_final: 0.9176 (tp) REVERT: B 453 TYR cc_start: 0.8914 (t80) cc_final: 0.8615 (t80) REVERT: B 528 THR cc_start: 0.9331 (p) cc_final: 0.8897 (t) REVERT: B 576 MET cc_start: 0.8086 (mtt) cc_final: 0.7880 (mtp) REVERT: B 579 GLN cc_start: 0.8797 (mm110) cc_final: 0.8368 (mt0) REVERT: B 584 PHE cc_start: 0.8729 (m-80) cc_final: 0.8512 (m-80) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.1567 time to fit residues: 55.7921 Evaluate side-chains 164 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 0.0170 chunk 113 optimal weight: 8.9990 chunk 119 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 overall best weight: 4.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 10312 Z= 0.362 Angle : 0.666 6.738 14008 Z= 0.339 Chirality : 0.042 0.138 1588 Planarity : 0.004 0.039 1742 Dihedral : 4.345 17.940 1370 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.88 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % 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: 0.64 (0.23), residues: 1250 helix: 1.14 (0.18), residues: 792 sheet: 0.59 (0.76), residues: 40 loop : -0.91 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 186 HIS 0.010 0.002 HIS A 390 PHE 0.038 0.002 PHE B 407 TYR 0.018 0.002 TYR B 308 ARG 0.003 0.001 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 MET cc_start: 0.8214 (mmm) cc_final: 0.7973 (mmt) REVERT: A 81 LEU cc_start: 0.8713 (mt) cc_final: 0.8289 (tp) REVERT: A 121 MET cc_start: 0.8139 (tpp) cc_final: 0.7872 (tpp) REVERT: A 125 GLN cc_start: 0.8909 (mt0) cc_final: 0.8708 (mt0) REVERT: A 217 TYR cc_start: 0.8888 (t80) cc_final: 0.8659 (t80) REVERT: A 270 TYR cc_start: 0.8949 (t80) cc_final: 0.8500 (t80) REVERT: A 373 MET cc_start: 0.8334 (ttp) cc_final: 0.7605 (tpp) REVERT: A 377 TYR cc_start: 0.9404 (t80) cc_final: 0.9154 (t80) REVERT: A 405 LEU cc_start: 0.9427 (tp) cc_final: 0.9152 (tp) REVERT: A 427 LYS cc_start: 0.8487 (pttt) cc_final: 0.8182 (tptp) REVERT: A 458 LYS cc_start: 0.8457 (mttt) cc_final: 0.8226 (mttp) REVERT: A 459 HIS cc_start: 0.8321 (t70) cc_final: 0.8093 (t70) REVERT: A 576 MET cc_start: 0.8151 (mtt) cc_final: 0.7927 (mtp) REVERT: B 81 LEU cc_start: 0.8774 (mt) cc_final: 0.8238 (tp) REVERT: B 176 SER cc_start: 0.8711 (p) cc_final: 0.8255 (t) REVERT: B 217 TYR cc_start: 0.8779 (t80) cc_final: 0.8462 (t80) REVERT: B 373 MET cc_start: 0.8446 (ttp) cc_final: 0.7958 (tpp) REVERT: B 427 LYS cc_start: 0.8336 (pttt) cc_final: 0.7851 (tptp) REVERT: B 528 THR cc_start: 0.9393 (p) cc_final: 0.8958 (t) REVERT: B 576 MET cc_start: 0.8203 (mtt) cc_final: 0.7928 (mtp) REVERT: B 579 GLN cc_start: 0.8968 (mm110) cc_final: 0.8369 (mt0) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.1796 time to fit residues: 59.3512 Evaluate side-chains 165 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 107 optimal weight: 20.0000 chunk 30 optimal weight: 0.0570 overall best weight: 2.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 ASN B 570 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10312 Z= 0.210 Angle : 0.548 8.647 14008 Z= 0.280 Chirality : 0.039 0.146 1588 Planarity : 0.003 0.037 1742 Dihedral : 4.116 17.135 1370 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.80 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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: 1.07 (0.24), residues: 1250 helix: 1.48 (0.19), residues: 792 sheet: 0.96 (0.79), residues: 40 loop : -0.77 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 186 HIS 0.005 0.001 HIS B 459 PHE 0.019 0.001 PHE B 611 TYR 0.016 0.001 TYR B 203 ARG 0.003 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.177 Fit side-chains revert: symmetry clash REVERT: A 81 LEU cc_start: 0.8725 (mt) cc_final: 0.8320 (tp) REVERT: A 121 MET cc_start: 0.8091 (tpp) cc_final: 0.7822 (tpp) REVERT: A 125 GLN cc_start: 0.8802 (mt0) cc_final: 0.8534 (mt0) REVERT: A 217 TYR cc_start: 0.8727 (t80) cc_final: 0.8431 (t80) REVERT: A 259 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7673 (mm-30) REVERT: A 270 TYR cc_start: 0.8890 (t80) cc_final: 0.8457 (t80) REVERT: A 373 MET cc_start: 0.8396 (ttm) cc_final: 0.7690 (tpp) REVERT: A 459 HIS cc_start: 0.8147 (t70) cc_final: 0.7890 (t70) REVERT: A 531 ASN cc_start: 0.8208 (m-40) cc_final: 0.7656 (t0) REVERT: A 576 MET cc_start: 0.8199 (mtt) cc_final: 0.7947 (mtp) REVERT: A 608 ILE cc_start: 0.9204 (mt) cc_final: 0.8999 (mm) REVERT: B 81 LEU cc_start: 0.8744 (mt) cc_final: 0.8238 (tp) REVERT: B 176 SER cc_start: 0.8664 (p) cc_final: 0.8306 (t) REVERT: B 217 TYR cc_start: 0.8619 (t80) cc_final: 0.8252 (t80) REVERT: B 237 TRP cc_start: 0.8591 (m-10) cc_final: 0.8314 (m-10) REVERT: B 270 TYR cc_start: 0.8992 (t80) cc_final: 0.8537 (t80) REVERT: B 373 MET cc_start: 0.8388 (ttp) cc_final: 0.7852 (tpp) REVERT: B 427 LYS cc_start: 0.8197 (pttt) cc_final: 0.7624 (tptp) REVERT: B 528 THR cc_start: 0.9196 (p) cc_final: 0.8685 (t) REVERT: B 576 MET cc_start: 0.8158 (mtt) cc_final: 0.7911 (mtp) REVERT: B 579 GLN cc_start: 0.8860 (mm110) cc_final: 0.8381 (mt0) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1592 time to fit residues: 54.4809 Evaluate side-chains 173 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 70 optimal weight: 0.3980 chunk 29 optimal weight: 9.9990 chunk 119 optimal weight: 0.5980 chunk 99 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 HIS B 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10312 Z= 0.142 Angle : 0.489 8.732 14008 Z= 0.249 Chirality : 0.037 0.136 1588 Planarity : 0.003 0.034 1742 Dihedral : 3.809 15.165 1370 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.48 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % 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: 1.38 (0.24), residues: 1250 helix: 1.68 (0.18), residues: 798 sheet: 1.14 (0.83), residues: 40 loop : -0.60 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 261 HIS 0.004 0.001 HIS B 459 PHE 0.031 0.001 PHE B 407 TYR 0.015 0.001 TYR A 203 ARG 0.003 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 1.177 Fit side-chains revert: symmetry clash REVERT: A 217 TYR cc_start: 0.8569 (t80) cc_final: 0.8189 (t80) REVERT: A 235 PHE cc_start: 0.7866 (m-10) cc_final: 0.7616 (t80) REVERT: A 259 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7566 (mm-30) REVERT: A 373 MET cc_start: 0.8291 (ttm) cc_final: 0.7600 (tpp) REVERT: A 459 HIS cc_start: 0.8062 (t70) cc_final: 0.7839 (t70) REVERT: A 528 THR cc_start: 0.9226 (p) cc_final: 0.8612 (t) REVERT: A 531 ASN cc_start: 0.8684 (m-40) cc_final: 0.7821 (t0) REVERT: A 576 MET cc_start: 0.8072 (mtt) cc_final: 0.7859 (mtp) REVERT: B 81 LEU cc_start: 0.8721 (mt) cc_final: 0.8202 (tp) REVERT: B 217 TYR cc_start: 0.8449 (t80) cc_final: 0.8038 (t80) REVERT: B 237 TRP cc_start: 0.8631 (m-10) cc_final: 0.8230 (m-10) REVERT: B 373 MET cc_start: 0.8333 (ttp) cc_final: 0.7725 (tpp) REVERT: B 427 LYS cc_start: 0.8128 (pttt) cc_final: 0.7545 (tptp) REVERT: B 528 THR cc_start: 0.9245 (p) cc_final: 0.8614 (t) REVERT: B 531 ASN cc_start: 0.8710 (m-40) cc_final: 0.7956 (t0) REVERT: B 576 MET cc_start: 0.8182 (mtt) cc_final: 0.7937 (mtp) REVERT: B 579 GLN cc_start: 0.8846 (mm110) cc_final: 0.8439 (mt0) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.1681 time to fit residues: 58.0774 Evaluate side-chains 174 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 72 optimal weight: 0.0170 chunk 55 optimal weight: 5.9990 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10312 Z= 0.166 Angle : 0.523 8.492 14008 Z= 0.263 Chirality : 0.038 0.166 1588 Planarity : 0.003 0.034 1742 Dihedral : 3.764 14.532 1370 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.48 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.24), residues: 1250 helix: 1.82 (0.18), residues: 796 sheet: 1.33 (0.86), residues: 40 loop : -0.49 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 261 HIS 0.004 0.001 HIS B 459 PHE 0.023 0.001 PHE A 611 TYR 0.020 0.001 TYR A 377 ARG 0.002 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: A 81 LEU cc_start: 0.8519 (mp) cc_final: 0.7862 (tp) REVERT: A 217 TYR cc_start: 0.8574 (t80) cc_final: 0.8236 (t80) REVERT: A 235 PHE cc_start: 0.7952 (m-10) cc_final: 0.7644 (t80) REVERT: A 259 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7589 (mm-30) REVERT: A 373 MET cc_start: 0.8405 (ttm) cc_final: 0.7625 (tpp) REVERT: A 427 LYS cc_start: 0.8240 (pttt) cc_final: 0.7772 (tptp) REVERT: A 459 HIS cc_start: 0.8045 (t70) cc_final: 0.7845 (t70) REVERT: A 528 THR cc_start: 0.9282 (p) cc_final: 0.8747 (t) REVERT: A 581 ASN cc_start: 0.8797 (m110) cc_final: 0.8296 (p0) REVERT: B 81 LEU cc_start: 0.8713 (mt) cc_final: 0.8141 (tt) REVERT: B 217 TYR cc_start: 0.8456 (t80) cc_final: 0.8048 (t80) REVERT: B 237 TRP cc_start: 0.8650 (m-10) cc_final: 0.8254 (m-10) REVERT: B 312 LEU cc_start: 0.9015 (tt) cc_final: 0.8655 (mt) REVERT: B 373 MET cc_start: 0.8406 (ttp) cc_final: 0.7852 (tpp) REVERT: B 427 LYS cc_start: 0.8089 (pttt) cc_final: 0.7375 (tptp) REVERT: B 528 THR cc_start: 0.9270 (p) cc_final: 0.8681 (t) REVERT: B 576 MET cc_start: 0.8167 (mtt) cc_final: 0.7954 (mtp) REVERT: B 579 GLN cc_start: 0.8826 (mm110) cc_final: 0.8451 (mt0) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1606 time to fit residues: 53.2211 Evaluate side-chains 172 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 0.1980 chunk 75 optimal weight: 10.0000 chunk 81 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10312 Z= 0.142 Angle : 0.506 7.749 14008 Z= 0.253 Chirality : 0.037 0.150 1588 Planarity : 0.003 0.033 1742 Dihedral : 3.689 14.100 1370 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.32 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: 1.71 (0.24), residues: 1250 helix: 1.93 (0.18), residues: 796 sheet: 1.29 (0.86), residues: 40 loop : -0.44 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 261 HIS 0.004 0.001 HIS B 459 PHE 0.034 0.001 PHE A 407 TYR 0.022 0.001 TYR B 308 ARG 0.003 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 70 TYR cc_start: 0.7100 (m-80) cc_final: 0.6662 (m-80) REVERT: A 81 LEU cc_start: 0.8517 (mp) cc_final: 0.7856 (tp) REVERT: A 217 TYR cc_start: 0.8489 (t80) cc_final: 0.8143 (t80) REVERT: A 235 PHE cc_start: 0.7954 (m-10) cc_final: 0.7635 (t80) REVERT: A 259 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7549 (mm-30) REVERT: A 373 MET cc_start: 0.8277 (ttm) cc_final: 0.7546 (tpp) REVERT: A 377 TYR cc_start: 0.9159 (t80) cc_final: 0.8847 (t80) REVERT: A 459 HIS cc_start: 0.8031 (t70) cc_final: 0.7822 (t70) REVERT: A 528 THR cc_start: 0.9299 (p) cc_final: 0.8782 (t) REVERT: A 581 ASN cc_start: 0.8816 (m110) cc_final: 0.8365 (p0) REVERT: B 81 LEU cc_start: 0.8682 (mt) cc_final: 0.8158 (tt) REVERT: B 217 TYR cc_start: 0.8434 (t80) cc_final: 0.8079 (t80) REVERT: B 237 TRP cc_start: 0.8250 (m-10) cc_final: 0.7902 (m-90) REVERT: B 312 LEU cc_start: 0.9012 (tt) cc_final: 0.8612 (mt) REVERT: B 373 MET cc_start: 0.8370 (ttp) cc_final: 0.7809 (tpp) REVERT: B 427 LYS cc_start: 0.8023 (pttt) cc_final: 0.7270 (tptp) REVERT: B 528 THR cc_start: 0.9303 (p) cc_final: 0.8728 (t) REVERT: B 576 MET cc_start: 0.8156 (mtt) cc_final: 0.7940 (mtp) REVERT: B 579 GLN cc_start: 0.8831 (mm110) cc_final: 0.8466 (mt0) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1602 time to fit residues: 54.7362 Evaluate side-chains 177 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 100 optimal weight: 0.3980 chunk 105 optimal weight: 0.6980 chunk 110 optimal weight: 0.2980 chunk 73 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 ASN B 399 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10312 Z= 0.152 Angle : 0.523 7.783 14008 Z= 0.260 Chirality : 0.037 0.215 1588 Planarity : 0.003 0.033 1742 Dihedral : 3.675 13.743 1370 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.92 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.24), residues: 1250 helix: 1.96 (0.18), residues: 798 sheet: 0.93 (0.86), residues: 40 loop : -0.37 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 186 HIS 0.004 0.001 HIS B 399 PHE 0.022 0.001 PHE B 383 TYR 0.027 0.001 TYR B 187 ARG 0.003 0.000 ARG B 539 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 1.157 Fit side-chains revert: symmetry clash REVERT: A 70 TYR cc_start: 0.7083 (m-80) cc_final: 0.6641 (m-80) REVERT: A 81 LEU cc_start: 0.8506 (mp) cc_final: 0.7886 (tt) REVERT: A 217 TYR cc_start: 0.8417 (t80) cc_final: 0.8113 (t80) REVERT: A 259 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7563 (mm-30) REVERT: A 373 MET cc_start: 0.8297 (ttm) cc_final: 0.7579 (tpp) REVERT: A 427 LYS cc_start: 0.8159 (pttt) cc_final: 0.7638 (tptp) REVERT: A 459 HIS cc_start: 0.8025 (t70) cc_final: 0.7804 (t70) REVERT: A 528 THR cc_start: 0.9316 (p) cc_final: 0.8800 (t) REVERT: A 581 ASN cc_start: 0.8806 (m110) cc_final: 0.8373 (p0) REVERT: B 70 TYR cc_start: 0.7142 (m-10) cc_final: 0.6808 (m-80) REVERT: B 81 LEU cc_start: 0.8718 (mt) cc_final: 0.8192 (tt) REVERT: B 121 MET cc_start: 0.8200 (tpp) cc_final: 0.7751 (tpp) REVERT: B 125 GLN cc_start: 0.8444 (mt0) cc_final: 0.8228 (mt0) REVERT: B 217 TYR cc_start: 0.8377 (t80) cc_final: 0.8028 (t80) REVERT: B 312 LEU cc_start: 0.8973 (tt) cc_final: 0.8576 (mt) REVERT: B 373 MET cc_start: 0.8370 (ttp) cc_final: 0.7834 (tpp) REVERT: B 427 LYS cc_start: 0.8018 (pttt) cc_final: 0.7213 (tptp) REVERT: B 528 THR cc_start: 0.9174 (p) cc_final: 0.8533 (t) REVERT: B 531 ASN cc_start: 0.8414 (m-40) cc_final: 0.7825 (t0) REVERT: B 576 MET cc_start: 0.8153 (mtt) cc_final: 0.7932 (mtp) REVERT: B 579 GLN cc_start: 0.8813 (mm110) cc_final: 0.8474 (mt0) REVERT: B 608 ILE cc_start: 0.9275 (mt) cc_final: 0.9057 (mm) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.1670 time to fit residues: 56.1916 Evaluate side-chains 183 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 75 optimal weight: 0.0570 chunk 60 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 ASN B 390 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10312 Z= 0.231 Angle : 0.565 8.841 14008 Z= 0.281 Chirality : 0.039 0.131 1588 Planarity : 0.003 0.033 1742 Dihedral : 3.745 13.832 1370 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.08 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.24), residues: 1250 helix: 1.95 (0.18), residues: 796 sheet: 1.14 (0.86), residues: 40 loop : -0.42 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 186 HIS 0.004 0.001 HIS B 399 PHE 0.023 0.002 PHE B 611 TYR 0.015 0.001 TYR A 377 ARG 0.003 0.000 ARG B 201 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 70 TYR cc_start: 0.7096 (m-80) cc_final: 0.6630 (m-80) REVERT: A 81 LEU cc_start: 0.8532 (mp) cc_final: 0.7894 (tt) REVERT: A 217 TYR cc_start: 0.8572 (t80) cc_final: 0.8282 (t80) REVERT: A 259 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7711 (mm-30) REVERT: A 270 TYR cc_start: 0.8766 (t80) cc_final: 0.8402 (t80) REVERT: A 373 MET cc_start: 0.8324 (ttm) cc_final: 0.7419 (tpp) REVERT: A 427 LYS cc_start: 0.8212 (pttt) cc_final: 0.7678 (tptp) REVERT: A 528 THR cc_start: 0.9327 (p) cc_final: 0.8802 (t) REVERT: A 581 ASN cc_start: 0.8814 (m110) cc_final: 0.8378 (p0) REVERT: B 81 LEU cc_start: 0.8692 (mt) cc_final: 0.8160 (tt) REVERT: B 217 TYR cc_start: 0.8495 (t80) cc_final: 0.8156 (t80) REVERT: B 235 PHE cc_start: 0.7639 (m-10) cc_final: 0.7429 (m-10) REVERT: B 237 TRP cc_start: 0.8503 (m-10) cc_final: 0.8091 (m-10) REVERT: B 270 TYR cc_start: 0.8799 (t80) cc_final: 0.8409 (t80) REVERT: B 281 PHE cc_start: 0.6694 (t80) cc_final: 0.6474 (t80) REVERT: B 308 TYR cc_start: 0.8291 (p90) cc_final: 0.8051 (p90) REVERT: B 312 LEU cc_start: 0.9042 (tt) cc_final: 0.8642 (mt) REVERT: B 363 SER cc_start: 0.8719 (t) cc_final: 0.8517 (p) REVERT: B 373 MET cc_start: 0.8406 (ttp) cc_final: 0.7739 (tpp) REVERT: B 427 LYS cc_start: 0.8027 (pttt) cc_final: 0.7235 (tptp) REVERT: B 435 THR cc_start: 0.9489 (p) cc_final: 0.9237 (t) REVERT: B 528 THR cc_start: 0.9261 (p) cc_final: 0.8624 (t) REVERT: B 579 GLN cc_start: 0.8896 (mm110) cc_final: 0.8502 (mt0) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1603 time to fit residues: 56.3821 Evaluate side-chains 182 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 0.3980 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 HIS ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.124716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.099213 restraints weight = 15561.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.101556 restraints weight = 10632.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.103175 restraints weight = 8265.726| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10312 Z= 0.184 Angle : 0.541 8.214 14008 Z= 0.270 Chirality : 0.038 0.140 1588 Planarity : 0.003 0.034 1742 Dihedral : 3.705 14.107 1370 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.32 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.24), residues: 1250 helix: 2.01 (0.18), residues: 796 sheet: 1.00 (0.88), residues: 40 loop : -0.43 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 186 HIS 0.007 0.001 HIS A 459 PHE 0.030 0.002 PHE A 521 TYR 0.023 0.001 TYR A 377 ARG 0.002 0.000 ARG B 201 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2002.60 seconds wall clock time: 36 minutes 47.05 seconds (2207.05 seconds total)