Starting phenix.real_space_refine on Fri Mar 15 08:23:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jun_36662/03_2024/8jun_36662_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jun_36662/03_2024/8jun_36662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jun_36662/03_2024/8jun_36662.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jun_36662/03_2024/8jun_36662.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jun_36662/03_2024/8jun_36662_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jun_36662/03_2024/8jun_36662_updated.pdb" } resolution = 2.38 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= -0.002 sd= 0.101 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 Zn 2 6.06 5 P 2 5.49 5 S 66 5.16 5 C 7338 2.51 5 N 1764 2.21 5 O 1926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 61": "OE1" <-> "OE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A ARG 334": "NH1" <-> "NH2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 652": "NH1" <-> "NH2" Residue "A ARG 662": "NH1" <-> "NH2" Residue "A ARG 734": "NH1" <-> "NH2" Residue "A GLU 737": "OE1" <-> "OE2" Residue "A GLU 774": "OE1" <-> "OE2" Residue "A GLU 781": "OE1" <-> "OE2" Residue "A ARG 820": "NH1" <-> "NH2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B GLU 232": "OE1" <-> "OE2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B ARG 334": "NH1" <-> "NH2" Residue "B ARG 524": "NH1" <-> "NH2" Residue "B PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 652": "NH1" <-> "NH2" Residue "B ARG 662": "NH1" <-> "NH2" Residue "B ARG 734": "NH1" <-> "NH2" Residue "B GLU 737": "OE1" <-> "OE2" Residue "B GLU 774": "OE1" <-> "OE2" Residue "B GLU 781": "OE1" <-> "OE2" Residue "B ARG 820": "NH1" <-> "NH2" 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: 11098 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5496 Classifications: {'peptide': 678} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 653} Chain breaks: 1 Chain: "B" Number of atoms: 5496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5496 Classifications: {'peptide': 678} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 653} Chain breaks: 1 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {' ZN': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {' ZN': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.09, per 1000 atoms: 0.55 Number of scatterers: 11098 At special positions: 0 Unit cell: (113.42, 118.77, 121.98, 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) Zn 2 29.99 S 66 16.00 P 2 15.00 O 1926 8.00 N 1764 7.00 C 7338 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 222 " distance=2.04 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 479 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 782 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 222 " distance=2.04 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 479 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 782 " distance=2.03 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: 4.32 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 563 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 791 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 795 " pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 563 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 791 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 795 " 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2600 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 10 sheets defined 44.0% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 303 through 332 removed outlier: 4.157A pdb=" N PHE A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 469 removed outlier: 3.761A pdb=" N THR A 450 " --> pdb=" O TRP A 446 " (cutoff:3.500A) Proline residue: A 458 - end of helix removed outlier: 3.558A pdb=" N LEU A 462 " --> pdb=" O PRO A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 527 removed outlier: 4.170A pdb=" N ASN A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU A 502 " --> pdb=" O ILE A 498 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLY A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N HIS A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 534 No H-bonds generated for 'chain 'A' and resid 531 through 534' Processing helix chain 'A' and resid 543 through 564 removed outlier: 3.782A pdb=" N ALA A 547 " --> pdb=" O GLY A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 574 removed outlier: 4.090A pdb=" N PHE A 571 " --> pdb=" O TYR A 568 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLN A 572 " --> pdb=" O SER A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 591 removed outlier: 3.839A pdb=" N MET A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 620 removed outlier: 3.753A pdb=" N SER A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N PHE A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 646 removed outlier: 3.691A pdb=" N ILE A 631 " --> pdb=" O TRP A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 667 removed outlier: 4.631A pdb=" N PHE A 667 " --> pdb=" O ALA A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 704 Processing helix chain 'A' and resid 709 through 734 Processing helix chain 'A' and resid 741 through 761 Processing helix chain 'A' and resid 772 through 778 removed outlier: 4.100A pdb=" N LYS A 778 " --> pdb=" O GLU A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 815 removed outlier: 5.418A pdb=" N ASP A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ASP A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ASP A 815 " --> pdb=" O THR A 811 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 252 No H-bonds generated for 'chain 'B' and resid 250 through 252' Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 303 through 332 removed outlier: 4.157A pdb=" N PHE B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 469 removed outlier: 3.761A pdb=" N THR B 450 " --> pdb=" O TRP B 446 " (cutoff:3.500A) Proline residue: B 458 - end of helix removed outlier: 3.568A pdb=" N LEU B 462 " --> pdb=" O PRO B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 527 removed outlier: 4.170A pdb=" N ASN B 501 " --> pdb=" O ASN B 497 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU B 502 " --> pdb=" O ILE B 498 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLY B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N HIS B 504 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 534 No H-bonds generated for 'chain 'B' and resid 531 through 534' Processing helix chain 'B' and resid 543 through 564 removed outlier: 3.783A pdb=" N ALA B 547 " --> pdb=" O GLY B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 574 removed outlier: 4.090A pdb=" N PHE B 571 " --> pdb=" O TYR B 568 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLN B 572 " --> pdb=" O SER B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 591 removed outlier: 3.840A pdb=" N MET B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 620 removed outlier: 3.753A pdb=" N SER B 607 " --> pdb=" O SER B 603 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N PHE B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 646 removed outlier: 3.691A pdb=" N ILE B 631 " --> pdb=" O TRP B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 667 removed outlier: 4.631A pdb=" N PHE B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 704 Processing helix chain 'B' and resid 709 through 734 Processing helix chain 'B' and resid 741 through 761 Processing helix chain 'B' and resid 772 through 778 removed outlier: 4.099A pdb=" N LYS B 778 " --> pdb=" O GLU B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 815 removed outlier: 5.417A pdb=" N ASP B 813 " --> pdb=" O LEU B 809 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ASP B 814 " --> pdb=" O LEU B 810 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ASP B 815 " --> pdb=" O THR B 811 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 51 through 56 removed outlier: 4.426A pdb=" N VAL A 78 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 62 through 70 Processing sheet with id= C, first strand: chain 'A' and resid 110 through 113 Processing sheet with id= D, first strand: chain 'A' and resid 177 through 181 Processing sheet with id= E, first strand: chain 'A' and resid 187 through 192 Processing sheet with id= F, first strand: chain 'B' and resid 51 through 56 removed outlier: 4.427A pdb=" N VAL B 78 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 62 through 70 Processing sheet with id= H, first strand: chain 'B' and resid 110 through 113 Processing sheet with id= I, first strand: chain 'B' and resid 177 through 181 Processing sheet with id= J, first strand: chain 'B' and resid 187 through 192 574 hydrogen bonds defined for protein. 1650 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: 3.29 Time building geometry restraints manager: 4.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1782 1.32 - 1.44: 3257 1.44 - 1.57: 6249 1.57 - 1.69: 4 1.69 - 1.81: 102 Bond restraints: 11394 Sorted by residual: bond pdb=" C31 POV A 902 " pdb=" O31 POV A 902 " ideal model delta sigma weight residual 1.327 1.464 -0.137 2.00e-02 2.50e+03 4.72e+01 bond pdb=" C21 POV B 902 " pdb=" O21 POV B 902 " ideal model delta sigma weight residual 1.330 1.437 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C21 POV A 902 " pdb=" O21 POV A 902 " ideal model delta sigma weight residual 1.330 1.431 -0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" C31 POV B 902 " pdb=" O31 POV B 902 " ideal model delta sigma weight residual 1.327 1.423 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" O12 POV A 902 " pdb=" P POV A 902 " ideal model delta sigma weight residual 1.657 1.610 0.047 2.00e-02 2.50e+03 5.56e+00 ... (remaining 11389 not shown) Histogram of bond angle deviations from ideal: 82.66 - 92.95: 5 92.95 - 103.24: 106 103.24 - 113.53: 6345 113.53 - 123.82: 8776 123.82 - 134.10: 240 Bond angle restraints: 15472 Sorted by residual: angle pdb=" C12 POV A 902 " pdb=" N POV A 902 " pdb=" C15 POV A 902 " ideal model delta sigma weight residual 112.10 82.66 29.44 3.00e+00 1.11e-01 9.63e+01 angle pdb=" C14 POV A 902 " pdb=" N POV A 902 " pdb=" C15 POV A 902 " ideal model delta sigma weight residual 108.02 82.86 25.16 3.00e+00 1.11e-01 7.03e+01 angle pdb=" C14 POV B 902 " pdb=" N POV B 902 " pdb=" C15 POV B 902 " ideal model delta sigma weight residual 108.02 83.47 24.55 3.00e+00 1.11e-01 6.70e+01 angle pdb=" C12 POV B 902 " pdb=" N POV B 902 " pdb=" C15 POV B 902 " ideal model delta sigma weight residual 112.10 89.38 22.72 3.00e+00 1.11e-01 5.73e+01 angle pdb=" N LEU A 462 " pdb=" CA LEU A 462 " pdb=" C LEU A 462 " ideal model delta sigma weight residual 111.07 118.58 -7.51 1.07e+00 8.73e-01 4.93e+01 ... (remaining 15467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.43: 6136 19.43 - 38.86: 434 38.86 - 58.30: 90 58.30 - 77.73: 28 77.73 - 97.16: 6 Dihedral angle restraints: 6694 sinusoidal: 2660 harmonic: 4034 Sorted by residual: dihedral pdb=" CA ASN A 570 " pdb=" C ASN A 570 " pdb=" N PHE A 571 " pdb=" CA PHE A 571 " ideal model delta harmonic sigma weight residual -180.00 -156.01 -23.99 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA ASN B 570 " pdb=" C ASN B 570 " pdb=" N PHE B 571 " pdb=" CA PHE B 571 " ideal model delta harmonic sigma weight residual 180.00 -156.05 -23.95 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA SER B 767 " pdb=" C SER B 767 " pdb=" N TRP B 768 " pdb=" CA TRP B 768 " ideal model delta harmonic sigma weight residual 180.00 157.71 22.29 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 6691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1260 0.047 - 0.095: 361 0.095 - 0.142: 99 0.142 - 0.189: 8 0.189 - 0.237: 4 Chirality restraints: 1732 Sorted by residual: chirality pdb=" CA LEU A 462 " pdb=" N LEU A 462 " pdb=" C LEU A 462 " pdb=" CB LEU A 462 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA TYR B 668 " pdb=" N TYR B 668 " pdb=" C TYR B 668 " pdb=" CB TYR B 668 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA TYR A 668 " pdb=" N TYR A 668 " pdb=" C TYR A 668 " pdb=" CB TYR A 668 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1729 not shown) Planarity restraints: 1920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 655 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.13e+00 pdb=" C ILE A 655 " 0.043 2.00e-02 2.50e+03 pdb=" O ILE A 655 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP A 656 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 655 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" C ILE B 655 " -0.042 2.00e-02 2.50e+03 pdb=" O ILE B 655 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP B 656 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 284 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" C THR B 284 " -0.036 2.00e-02 2.50e+03 pdb=" O THR B 284 " 0.014 2.00e-02 2.50e+03 pdb=" N TRP B 285 " 0.012 2.00e-02 2.50e+03 ... (remaining 1917 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 54 2.57 - 3.15: 9039 3.15 - 3.73: 17049 3.73 - 4.32: 25755 4.32 - 4.90: 41169 Nonbonded interactions: 93066 Sorted by model distance: nonbonded pdb=" C11 POV B 902 " pdb=" C15 POV B 902 " model vdw 1.983 3.088 nonbonded pdb=" C11 POV A 902 " pdb=" C15 POV A 902 " model vdw 2.050 3.088 nonbonded pdb=" OD1 ASP A 574 " pdb="ZN ZN A 901 " model vdw 2.070 2.230 nonbonded pdb=" OD1 ASP B 574 " pdb="ZN ZN B 901 " model vdw 2.071 2.230 nonbonded pdb=" O GLU B 124 " pdb=" OG SER B 184 " model vdw 2.181 2.440 ... (remaining 93061 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 individual isotropic 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 3.430 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 32.880 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 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:13.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 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 : 0.007 0.137 11394 Z= 0.446 Angle : 1.000 29.441 15472 Z= 0.475 Chirality : 0.048 0.237 1732 Planarity : 0.004 0.038 1920 Dihedral : 14.892 97.160 4070 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.69 (0.21), residues: 1348 helix: -0.70 (0.20), residues: 560 sheet: 0.72 (0.28), residues: 278 loop : -2.66 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 629 HIS 0.004 0.001 HIS A 487 PHE 0.018 0.002 PHE B 697 TYR 0.026 0.002 TYR A 680 ARG 0.008 0.001 ARG A 821 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6293 (mmm-85) cc_final: 0.5645 (ttm170) REVERT: A 118 ARG cc_start: 0.7337 (ttm110) cc_final: 0.7120 (ttt90) REVERT: A 145 ILE cc_start: 0.9085 (mt) cc_final: 0.8876 (mp) REVERT: A 641 LEU cc_start: 0.7522 (tp) cc_final: 0.7165 (mt) REVERT: B 44 ARG cc_start: 0.6878 (mmm-85) cc_final: 0.6304 (tmt170) REVERT: B 101 LYS cc_start: 0.8885 (mtmm) cc_final: 0.8648 (mtpp) REVERT: B 115 LEU cc_start: 0.8438 (mt) cc_final: 0.8232 (mt) REVERT: B 152 MET cc_start: 0.8624 (mtt) cc_final: 0.8349 (mtt) REVERT: B 222 CYS cc_start: 0.7374 (m) cc_final: 0.6953 (m) REVERT: B 240 MET cc_start: 0.9162 (ttt) cc_final: 0.8885 (ttt) REVERT: B 617 LEU cc_start: 0.7840 (mt) cc_final: 0.7594 (mm) REVERT: B 623 LYS cc_start: 0.7764 (mptt) cc_final: 0.7381 (mmtm) REVERT: B 652 ARG cc_start: 0.6905 (mmt180) cc_final: 0.5815 (mtt180) REVERT: B 783 ILE cc_start: 0.8371 (tt) cc_final: 0.8164 (pt) outliers start: 0 outliers final: 1 residues processed: 193 average time/residue: 1.0770 time to fit residues: 226.8017 Evaluate side-chains 144 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 143 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 625 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 504 HIS A 591 GLN A 763 GLN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN B 117 GLN B 142 GLN B 185 GLN B 504 HIS B 541 HIS B 591 GLN B 673 GLN B 691 ASN B 694 ASN B 763 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11394 Z= 0.239 Angle : 0.547 7.579 15472 Z= 0.293 Chirality : 0.044 0.152 1732 Planarity : 0.004 0.034 1920 Dihedral : 9.735 104.878 1572 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.82 % Allowed : 8.86 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.16 (0.22), residues: 1348 helix: 0.76 (0.21), residues: 592 sheet: 1.19 (0.28), residues: 278 loop : -2.07 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 629 HIS 0.005 0.001 HIS B 594 PHE 0.014 0.002 PHE B 632 TYR 0.017 0.002 TYR A 680 ARG 0.004 0.000 ARG B 821 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 151 time to evaluate : 1.197 Fit side-chains revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6281 (mmm-85) cc_final: 0.5735 (ttm170) REVERT: A 145 ILE cc_start: 0.9036 (mt) cc_final: 0.8798 (mp) REVERT: A 536 TYR cc_start: 0.7178 (m-80) cc_final: 0.6900 (m-80) REVERT: A 650 MET cc_start: 0.6894 (mtt) cc_final: 0.6594 (mtt) REVERT: B 44 ARG cc_start: 0.7009 (mmm-85) cc_final: 0.6397 (tmt170) REVERT: B 83 ASN cc_start: 0.7610 (p0) cc_final: 0.7316 (p0) REVERT: B 143 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.7841 (mm110) REVERT: B 536 TYR cc_start: 0.7853 (m-80) cc_final: 0.7529 (m-80) REVERT: B 548 MET cc_start: 0.8457 (mtt) cc_final: 0.8180 (mtp) REVERT: B 617 LEU cc_start: 0.7861 (mt) cc_final: 0.7634 (mm) REVERT: B 623 LYS cc_start: 0.7352 (mptt) cc_final: 0.7104 (mmtm) REVERT: B 652 ARG cc_start: 0.6411 (mmt180) cc_final: 0.5305 (mtm180) REVERT: B 684 MET cc_start: 0.8097 (mmm) cc_final: 0.7849 (tpt) outliers start: 22 outliers final: 7 residues processed: 165 average time/residue: 1.0215 time to fit residues: 184.2943 Evaluate side-chains 141 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 133 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 696 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 120 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN B 113 GLN B 497 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 11394 Z= 0.527 Angle : 0.689 6.620 15472 Z= 0.365 Chirality : 0.050 0.255 1732 Planarity : 0.005 0.054 1920 Dihedral : 9.604 92.551 1570 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.65 % Allowed : 11.01 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.01 (0.22), residues: 1348 helix: 0.78 (0.21), residues: 590 sheet: 1.35 (0.28), residues: 282 loop : -1.89 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 629 HIS 0.005 0.001 HIS B 229 PHE 0.021 0.003 PHE B 632 TYR 0.023 0.003 TYR A 724 ARG 0.005 0.001 ARG A 593 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 144 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6279 (mmm-85) cc_final: 0.5764 (ttp-170) REVERT: A 63 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8018 (tp) REVERT: A 90 ASN cc_start: 0.8058 (m-40) cc_final: 0.7743 (m-40) REVERT: A 143 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8001 (mt0) REVERT: A 145 ILE cc_start: 0.9056 (mt) cc_final: 0.8796 (mp) REVERT: A 536 TYR cc_start: 0.7478 (m-80) cc_final: 0.7022 (m-80) REVERT: A 650 MET cc_start: 0.6994 (mtt) cc_final: 0.6496 (mtp) REVERT: B 536 TYR cc_start: 0.7765 (m-80) cc_final: 0.7499 (m-80) REVERT: B 617 LEU cc_start: 0.7878 (mt) cc_final: 0.7580 (mm) REVERT: B 621 PHE cc_start: 0.8537 (m-80) cc_final: 0.8305 (m-80) REVERT: B 623 LYS cc_start: 0.7986 (mptt) cc_final: 0.7766 (mmtm) REVERT: B 650 MET cc_start: 0.6834 (OUTLIER) cc_final: 0.6345 (mtt) REVERT: B 652 ARG cc_start: 0.7072 (mmt180) cc_final: 0.5851 (mtt180) REVERT: B 700 PHE cc_start: 0.6500 (t80) cc_final: 0.6298 (t80) REVERT: B 704 TYR cc_start: 0.7766 (m-80) cc_final: 0.7446 (m-80) REVERT: B 738 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7785 (ptpt) outliers start: 32 outliers final: 13 residues processed: 163 average time/residue: 1.0882 time to fit residues: 193.3933 Evaluate side-chains 148 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 821 ARG Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain B residue 738 LYS Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 822 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 58 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 HIS ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN B 142 GLN B 447 ASN B 673 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11394 Z= 0.225 Angle : 0.517 5.917 15472 Z= 0.277 Chirality : 0.043 0.160 1732 Planarity : 0.003 0.037 1920 Dihedral : 8.813 86.363 1570 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.65 % Allowed : 12.00 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.34 (0.23), residues: 1348 helix: 1.12 (0.21), residues: 604 sheet: 1.50 (0.28), residues: 278 loop : -1.83 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 446 HIS 0.005 0.001 HIS B 594 PHE 0.013 0.001 PHE B 632 TYR 0.014 0.002 TYR B 210 ARG 0.005 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 148 time to evaluate : 1.391 Fit side-chains revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.7896 (tp) REVERT: A 90 ASN cc_start: 0.7987 (m-40) cc_final: 0.7685 (m-40) REVERT: A 143 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.7972 (mt0) REVERT: A 145 ILE cc_start: 0.9030 (mt) cc_final: 0.8777 (mp) REVERT: A 536 TYR cc_start: 0.7413 (m-80) cc_final: 0.7009 (m-80) REVERT: A 540 LYS cc_start: 0.8128 (mttm) cc_final: 0.7864 (mmtt) REVERT: A 554 MET cc_start: 0.7383 (tpp) cc_final: 0.7058 (mmt) REVERT: B 83 ASN cc_start: 0.7795 (p0) cc_final: 0.7483 (p0) REVERT: B 118 ARG cc_start: 0.7534 (ttm-80) cc_final: 0.7248 (mtp180) REVERT: B 548 MET cc_start: 0.8405 (mtm) cc_final: 0.8175 (mtp) REVERT: B 617 LEU cc_start: 0.7835 (mt) cc_final: 0.7612 (mm) REVERT: B 623 LYS cc_start: 0.7667 (mptt) cc_final: 0.7375 (mmtm) REVERT: B 650 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.6380 (mtt) REVERT: B 652 ARG cc_start: 0.7019 (mmt180) cc_final: 0.5797 (mtm110) outliers start: 32 outliers final: 15 residues processed: 164 average time/residue: 0.9875 time to fit residues: 178.2863 Evaluate side-chains 158 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 140 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain B residue 696 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 2.9990 chunk 1 optimal weight: 0.0570 chunk 96 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 110 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 overall best weight: 1.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN B 447 ASN B 673 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11394 Z= 0.205 Angle : 0.506 6.162 15472 Z= 0.270 Chirality : 0.042 0.155 1732 Planarity : 0.003 0.035 1920 Dihedral : 8.461 83.989 1570 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.32 % Allowed : 12.58 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.48 (0.23), residues: 1348 helix: 1.31 (0.21), residues: 604 sheet: 1.48 (0.28), residues: 282 loop : -1.85 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 629 HIS 0.005 0.001 HIS B 594 PHE 0.012 0.001 PHE B 632 TYR 0.013 0.001 TYR A 188 ARG 0.004 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 147 time to evaluate : 1.220 Fit side-chains revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8371 (mm) cc_final: 0.7796 (tp) REVERT: A 90 ASN cc_start: 0.7972 (m-40) cc_final: 0.7684 (m-40) REVERT: A 143 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.7959 (mt0) REVERT: A 145 ILE cc_start: 0.9025 (mt) cc_final: 0.8778 (mp) REVERT: A 536 TYR cc_start: 0.7390 (m-80) cc_final: 0.7017 (m-80) REVERT: A 540 LYS cc_start: 0.8184 (mttm) cc_final: 0.7896 (mmtt) REVERT: A 554 MET cc_start: 0.7335 (tpp) cc_final: 0.7075 (mmt) REVERT: A 650 MET cc_start: 0.7187 (mtp) cc_final: 0.6984 (mtp) REVERT: B 71 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7602 (mp-120) REVERT: B 83 ASN cc_start: 0.7830 (p0) cc_final: 0.7515 (p0) REVERT: B 118 ARG cc_start: 0.7574 (ttm-80) cc_final: 0.7345 (ttt-90) REVERT: B 221 MET cc_start: 0.7102 (OUTLIER) cc_final: 0.6768 (mpm) REVERT: B 276 PHE cc_start: 0.5680 (OUTLIER) cc_final: 0.4772 (t80) REVERT: B 443 ILE cc_start: 0.7556 (mp) cc_final: 0.7328 (mp) REVERT: B 447 ASN cc_start: 0.7081 (m-40) cc_final: 0.6872 (m110) REVERT: B 548 MET cc_start: 0.8395 (mtm) cc_final: 0.8172 (mtp) REVERT: B 621 PHE cc_start: 0.8501 (m-80) cc_final: 0.8260 (m-80) REVERT: B 652 ARG cc_start: 0.7034 (mmt180) cc_final: 0.5812 (mtm110) REVERT: B 704 TYR cc_start: 0.7763 (m-80) cc_final: 0.7477 (m-80) outliers start: 28 outliers final: 14 residues processed: 165 average time/residue: 1.0344 time to fit residues: 187.3851 Evaluate side-chains 160 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 143 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 822 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 278 GLN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 11394 Z= 0.542 Angle : 0.676 8.446 15472 Z= 0.356 Chirality : 0.050 0.264 1732 Planarity : 0.005 0.057 1920 Dihedral : 9.029 91.867 1570 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.65 % Allowed : 12.42 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.22 (0.22), residues: 1348 helix: 0.90 (0.20), residues: 608 sheet: 1.47 (0.28), residues: 282 loop : -1.80 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 629 HIS 0.004 0.001 HIS B 795 PHE 0.022 0.003 PHE B 632 TYR 0.023 0.003 TYR A 724 ARG 0.005 0.001 ARG A 821 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 142 time to evaluate : 1.147 Fit side-chains revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.7980 (tp) REVERT: A 90 ASN cc_start: 0.8081 (m-40) cc_final: 0.7796 (m-40) REVERT: A 143 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.7986 (mt0) REVERT: A 145 ILE cc_start: 0.9062 (mt) cc_final: 0.8801 (mp) REVERT: A 278 GLN cc_start: 0.4185 (OUTLIER) cc_final: 0.3893 (tm-30) REVERT: A 536 TYR cc_start: 0.7457 (m-80) cc_final: 0.7047 (m-80) REVERT: A 540 LYS cc_start: 0.8211 (mttm) cc_final: 0.7872 (mmmt) REVERT: A 554 MET cc_start: 0.7411 (tpp) cc_final: 0.7075 (mmt) REVERT: A 602 TYR cc_start: 0.4381 (OUTLIER) cc_final: 0.3060 (m-80) REVERT: A 700 PHE cc_start: 0.6663 (m-10) cc_final: 0.6430 (m-80) REVERT: B 118 ARG cc_start: 0.7608 (ttm-80) cc_final: 0.7304 (mtp180) REVERT: B 207 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7327 (mp0) REVERT: B 276 PHE cc_start: 0.6359 (OUTLIER) cc_final: 0.5566 (t80) REVERT: B 621 PHE cc_start: 0.8568 (m-80) cc_final: 0.8292 (m-80) REVERT: B 652 ARG cc_start: 0.7245 (mmt180) cc_final: 0.6795 (mpt180) REVERT: B 704 TYR cc_start: 0.7778 (m-80) cc_final: 0.7567 (m-80) outliers start: 32 outliers final: 15 residues processed: 162 average time/residue: 0.9976 time to fit residues: 177.4305 Evaluate side-chains 157 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 623 LYS Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 696 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN B 447 ASN B 673 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11394 Z= 0.173 Angle : 0.505 6.675 15472 Z= 0.269 Chirality : 0.042 0.173 1732 Planarity : 0.003 0.036 1920 Dihedral : 8.568 84.492 1570 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.99 % Allowed : 13.49 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.58 (0.23), residues: 1348 helix: 1.36 (0.21), residues: 604 sheet: 1.50 (0.28), residues: 282 loop : -1.73 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 629 HIS 0.006 0.001 HIS B 594 PHE 0.013 0.001 PHE B 632 TYR 0.016 0.001 TYR A 210 ARG 0.005 0.000 ARG A 821 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.7816 (tp) REVERT: A 90 ASN cc_start: 0.8051 (m-40) cc_final: 0.7752 (m-40) REVERT: A 143 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.7994 (mt0) REVERT: A 145 ILE cc_start: 0.9037 (mt) cc_final: 0.8795 (mp) REVERT: A 536 TYR cc_start: 0.7389 (m-80) cc_final: 0.7023 (m-80) REVERT: A 540 LYS cc_start: 0.8114 (mttm) cc_final: 0.7827 (mmmt) REVERT: A 554 MET cc_start: 0.7260 (tpp) cc_final: 0.7026 (mmt) REVERT: A 602 TYR cc_start: 0.4342 (OUTLIER) cc_final: 0.3118 (m-80) REVERT: A 700 PHE cc_start: 0.6588 (m-10) cc_final: 0.6361 (m-80) REVERT: B 71 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7658 (mp-120) REVERT: B 83 ASN cc_start: 0.7751 (p0) cc_final: 0.7506 (p0) REVERT: B 118 ARG cc_start: 0.7560 (ttm-80) cc_final: 0.7305 (mtp180) REVERT: B 276 PHE cc_start: 0.5705 (OUTLIER) cc_final: 0.4883 (t80) REVERT: B 446 TRP cc_start: 0.6040 (OUTLIER) cc_final: 0.5528 (m100) REVERT: B 621 PHE cc_start: 0.8489 (m-80) cc_final: 0.8268 (m-80) REVERT: B 652 ARG cc_start: 0.6948 (mmt180) cc_final: 0.6455 (mpt180) REVERT: B 704 TYR cc_start: 0.7762 (m-80) cc_final: 0.7528 (m-80) REVERT: B 821 ARG cc_start: 0.6778 (mmp-170) cc_final: 0.6545 (mmp-170) outliers start: 24 outliers final: 14 residues processed: 161 average time/residue: 0.9989 time to fit residues: 177.5686 Evaluate side-chains 159 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 140 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 696 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 25 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN B 447 ASN B 673 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 11394 Z= 0.329 Angle : 0.571 6.112 15472 Z= 0.304 Chirality : 0.045 0.202 1732 Planarity : 0.004 0.043 1920 Dihedral : 8.648 86.507 1570 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.40 % Allowed : 13.58 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 (0.23), residues: 1348 helix: 1.23 (0.21), residues: 606 sheet: 1.58 (0.28), residues: 282 loop : -1.65 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 629 HIS 0.004 0.001 HIS B 594 PHE 0.017 0.002 PHE B 632 TYR 0.015 0.002 TYR A 188 ARG 0.004 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.7840 (tp) REVERT: A 90 ASN cc_start: 0.8045 (m-40) cc_final: 0.7771 (m-40) REVERT: A 143 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.7963 (mt0) REVERT: A 145 ILE cc_start: 0.9051 (mt) cc_final: 0.8798 (mp) REVERT: A 536 TYR cc_start: 0.7447 (m-80) cc_final: 0.7078 (m-80) REVERT: A 540 LYS cc_start: 0.8108 (mttm) cc_final: 0.7831 (mmmt) REVERT: A 554 MET cc_start: 0.7316 (tpp) cc_final: 0.7046 (mmt) REVERT: A 602 TYR cc_start: 0.4261 (OUTLIER) cc_final: 0.3716 (t80) REVERT: A 613 MET cc_start: 0.7195 (tpt) cc_final: 0.6845 (mmm) REVERT: A 700 PHE cc_start: 0.6624 (m-10) cc_final: 0.6393 (m-80) REVERT: B 118 ARG cc_start: 0.7589 (ttm-80) cc_final: 0.7285 (mtp180) REVERT: B 276 PHE cc_start: 0.6073 (OUTLIER) cc_final: 0.5238 (t80) REVERT: B 446 TRP cc_start: 0.6082 (OUTLIER) cc_final: 0.5501 (m100) REVERT: B 621 PHE cc_start: 0.8490 (m-80) cc_final: 0.8235 (m-80) REVERT: B 652 ARG cc_start: 0.7041 (mmt180) cc_final: 0.6629 (mpt180) REVERT: B 704 TYR cc_start: 0.7795 (m-80) cc_final: 0.7573 (m-80) outliers start: 29 outliers final: 17 residues processed: 160 average time/residue: 1.0003 time to fit residues: 175.9448 Evaluate side-chains 160 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 138 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 696 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 6.9990 chunk 123 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 0.0970 chunk 94 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 119 optimal weight: 0.0980 chunk 79 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN B 158 GLN B 673 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 11394 Z= 0.149 Angle : 0.489 6.325 15472 Z= 0.260 Chirality : 0.042 0.145 1732 Planarity : 0.003 0.034 1920 Dihedral : 8.135 81.903 1570 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.99 % Allowed : 13.82 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.71 (0.23), residues: 1348 helix: 1.46 (0.21), residues: 608 sheet: 1.56 (0.28), residues: 282 loop : -1.67 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 629 HIS 0.005 0.001 HIS B 594 PHE 0.013 0.001 PHE B 632 TYR 0.013 0.001 TYR A 210 ARG 0.004 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.8034 (m-40) cc_final: 0.7757 (m-40) REVERT: A 145 ILE cc_start: 0.9022 (mt) cc_final: 0.8783 (mp) REVERT: A 536 TYR cc_start: 0.7345 (m-80) cc_final: 0.7047 (m-80) REVERT: A 540 LYS cc_start: 0.8093 (mttm) cc_final: 0.7839 (mmmt) REVERT: A 602 TYR cc_start: 0.4166 (OUTLIER) cc_final: 0.3825 (t80) REVERT: A 613 MET cc_start: 0.7212 (tpt) cc_final: 0.6888 (mmm) REVERT: B 58 LEU cc_start: 0.9140 (tp) cc_final: 0.8895 (tm) REVERT: B 71 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7693 (mp-120) REVERT: B 83 ASN cc_start: 0.7586 (p0) cc_final: 0.7379 (p0) REVERT: B 118 ARG cc_start: 0.7585 (ttm-80) cc_final: 0.7308 (ttt-90) REVERT: B 133 GLU cc_start: 0.7133 (tt0) cc_final: 0.6874 (tt0) REVERT: B 276 PHE cc_start: 0.5603 (OUTLIER) cc_final: 0.4677 (t80) REVERT: B 446 TRP cc_start: 0.6118 (OUTLIER) cc_final: 0.5476 (m100) REVERT: B 652 ARG cc_start: 0.6853 (mmt180) cc_final: 0.6433 (mpt180) REVERT: B 704 TYR cc_start: 0.7734 (m-80) cc_final: 0.7500 (m-80) outliers start: 24 outliers final: 13 residues processed: 160 average time/residue: 0.9537 time to fit residues: 168.7806 Evaluate side-chains 151 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 135 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 613 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN B 673 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11394 Z= 0.311 Angle : 0.571 6.830 15472 Z= 0.302 Chirality : 0.045 0.199 1732 Planarity : 0.004 0.041 1920 Dihedral : 8.347 84.601 1570 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.32 % Allowed : 14.65 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 (0.23), residues: 1348 helix: 1.33 (0.21), residues: 606 sheet: 1.66 (0.28), residues: 282 loop : -1.57 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 629 HIS 0.004 0.001 HIS B 594 PHE 0.016 0.002 PHE B 632 TYR 0.014 0.002 TYR A 188 ARG 0.004 0.000 ARG A 821 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 137 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.8042 (m-40) cc_final: 0.7775 (m-40) REVERT: A 145 ILE cc_start: 0.9051 (mt) cc_final: 0.8801 (mp) REVERT: A 536 TYR cc_start: 0.7368 (m-80) cc_final: 0.7058 (m-80) REVERT: A 540 LYS cc_start: 0.8088 (mttm) cc_final: 0.7831 (mmmt) REVERT: A 602 TYR cc_start: 0.4121 (OUTLIER) cc_final: 0.3655 (t80) REVERT: A 613 MET cc_start: 0.7193 (tpt) cc_final: 0.6847 (mmm) REVERT: B 83 ASN cc_start: 0.7863 (p0) cc_final: 0.7499 (p0) REVERT: B 118 ARG cc_start: 0.7565 (ttm-80) cc_final: 0.7326 (ttt-90) REVERT: B 195 LYS cc_start: 0.8672 (mppt) cc_final: 0.8427 (tppt) REVERT: B 276 PHE cc_start: 0.5918 (OUTLIER) cc_final: 0.4960 (t80) REVERT: B 446 TRP cc_start: 0.6178 (OUTLIER) cc_final: 0.5538 (m100) REVERT: B 652 ARG cc_start: 0.7030 (mmt180) cc_final: 0.6609 (mpt180) outliers start: 16 outliers final: 13 residues processed: 150 average time/residue: 1.0213 time to fit residues: 168.3846 Evaluate side-chains 151 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 135 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 613 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 106 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN B 158 GLN B 673 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.158423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.109224 restraints weight = 12868.157| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.21 r_work: 0.3389 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11394 Z= 0.208 Angle : 0.527 6.962 15472 Z= 0.279 Chirality : 0.043 0.163 1732 Planarity : 0.003 0.036 1920 Dihedral : 8.155 82.530 1570 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.49 % Allowed : 14.74 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.68 (0.23), residues: 1348 helix: 1.39 (0.21), residues: 606 sheet: 1.57 (0.28), residues: 282 loop : -1.63 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 629 HIS 0.005 0.001 HIS B 594 PHE 0.013 0.001 PHE B 632 TYR 0.014 0.001 TYR A 188 ARG 0.004 0.000 ARG A 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3924.50 seconds wall clock time: 70 minutes 0.08 seconds (4200.08 seconds total)