Starting phenix.real_space_refine on Sat Dec 9 12:39:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jun_36662/12_2023/8jun_36662_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jun_36662/12_2023/8jun_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_36662/12_2023/8jun_36662.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jun_36662/12_2023/8jun_36662.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jun_36662/12_2023/8jun_36662_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jun_36662/12_2023/8jun_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-1.21rc1-5172/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: 6.20, per 1000 atoms: 0.56 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: 4.40 Conformation dependent library (CDL) restraints added in 2.1 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: 2.36 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: 3.26 Time building geometry restraints manager: 4.68 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: 1.080 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: 3.610 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 33.860 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:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.700 ------------------------------------------------------------------------------- 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 : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 193 average time/residue: 1.1061 time to fit residues: 233.1918 Evaluate side-chains 142 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 1.129 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2237 time to fit residues: 1.8867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 105 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 11394 Z= 0.295 Angle : 0.575 7.299 15472 Z= 0.309 Chirality : 0.045 0.179 1732 Planarity : 0.004 0.037 1920 Dihedral : 9.471 85.004 1570 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.24 % Allowed : 9.44 % Favored : 88.33 % 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: -0.25 (0.22), residues: 1348 helix: 0.67 (0.21), residues: 590 sheet: 1.17 (0.28), residues: 278 loop : -2.09 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 629 HIS 0.004 0.001 HIS B 594 PHE 0.013 0.002 PHE A 632 TYR 0.017 0.002 TYR A 680 ARG 0.006 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 176 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 8 residues processed: 162 average time/residue: 1.0369 time to fit residues: 184.2151 Evaluate side-chains 143 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 135 time to evaluate : 0.965 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.6997 time to fit residues: 2.8292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0970 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: 4.9990 chunk 120 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 ASN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN B 113 GLN B 117 GLN B 497 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 11394 Z= 0.424 Angle : 0.633 6.301 15472 Z= 0.337 Chirality : 0.048 0.228 1732 Planarity : 0.004 0.049 1920 Dihedral : 9.412 90.974 1570 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.90 % Allowed : 11.26 % Favored : 85.84 % 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: 0.02 (0.22), residues: 1348 helix: 0.81 (0.21), residues: 602 sheet: 1.34 (0.28), residues: 278 loop : -1.92 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 629 HIS 0.004 0.001 HIS B 594 PHE 0.017 0.002 PHE B 253 TYR 0.022 0.002 TYR A 724 ARG 0.003 0.000 ARG A 821 *********************** 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 186 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 151 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 17 residues processed: 167 average time/residue: 1.1234 time to fit residues: 205.0004 Evaluate side-chains 154 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 1.181 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 11 residues processed: 7 average time/residue: 0.5310 time to fit residues: 6.0274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 129 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN A 691 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11394 Z= 0.220 Angle : 0.527 6.813 15472 Z= 0.280 Chirality : 0.043 0.163 1732 Planarity : 0.003 0.036 1920 Dihedral : 8.828 86.029 1570 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.48 % Allowed : 12.91 % Favored : 84.60 % 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: 0.37 (0.23), residues: 1348 helix: 1.16 (0.21), residues: 604 sheet: 1.48 (0.28), residues: 278 loop : -1.82 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 446 HIS 0.006 0.001 HIS B 594 PHE 0.010 0.001 PHE B 445 TYR 0.014 0.001 TYR A 188 ARG 0.003 0.000 ARG A 118 *********************** 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 175 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 145 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 19 residues processed: 162 average time/residue: 1.0413 time to fit residues: 185.9433 Evaluate side-chains 158 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 139 time to evaluate : 1.223 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 13 residues processed: 8 average time/residue: 0.5874 time to fit residues: 6.9784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 0.0770 chunk 1 optimal weight: 0.0270 chunk 96 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 110 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN A 691 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11394 Z= 0.165 Angle : 0.488 6.324 15472 Z= 0.259 Chirality : 0.042 0.141 1732 Planarity : 0.003 0.033 1920 Dihedral : 8.438 82.230 1570 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.32 % Allowed : 13.49 % 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: 0.58 (0.23), residues: 1348 helix: 1.42 (0.21), residues: 604 sheet: 1.50 (0.28), residues: 282 loop : -1.81 (0.27), residues: 462 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 0.014 0.001 PHE B 632 TYR 0.012 0.001 TYR A 188 ARG 0.004 0.000 ARG B 118 *********************** 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 173 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 145 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 16 residues processed: 161 average time/residue: 0.9704 time to fit residues: 173.2106 Evaluate side-chains 153 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 137 time to evaluate : 1.111 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 4 average time/residue: 0.1248 time to fit residues: 2.4816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 76 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 124 optimal weight: 0.6980 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 497 ASN A 691 ASN ** 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: 0.7966 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 11394 Z= 0.481 Angle : 0.643 6.001 15472 Z= 0.341 Chirality : 0.049 0.242 1732 Planarity : 0.004 0.051 1920 Dihedral : 8.901 90.279 1570 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.40 % Allowed : 13.66 % Favored : 83.94 % 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: 0.30 (0.22), residues: 1348 helix: 0.99 (0.20), residues: 610 sheet: 1.52 (0.28), residues: 282 loop : -1.80 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 629 HIS 0.004 0.001 HIS B 795 PHE 0.020 0.002 PHE B 632 TYR 0.021 0.002 TYR A 724 ARG 0.005 0.001 ARG B 44 *********************** 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 167 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 138 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 18 residues processed: 158 average time/residue: 1.0326 time to fit residues: 179.7954 Evaluate side-chains 148 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 1.258 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 5 average time/residue: 0.7051 time to fit residues: 5.6496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.0970 chunk 73 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 129 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 79 optimal weight: 0.4980 chunk 51 optimal weight: 0.5980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 497 ASN A 691 ASN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 11394 Z= 0.151 Angle : 0.492 6.683 15472 Z= 0.261 Chirality : 0.042 0.141 1732 Planarity : 0.003 0.034 1920 Dihedral : 8.537 85.538 1570 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.99 % Allowed : 14.24 % 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: 0.64 (0.23), residues: 1348 helix: 1.44 (0.21), residues: 604 sheet: 1.55 (0.29), residues: 282 loop : -1.76 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 446 HIS 0.005 0.001 HIS B 594 PHE 0.014 0.001 PHE B 632 TYR 0.019 0.001 TYR A 602 ARG 0.004 0.000 ARG B 44 *********************** 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 162 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 1.248 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 15 residues processed: 153 average time/residue: 1.0160 time to fit residues: 172.3557 Evaluate side-chains 147 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 1.218 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 5 average time/residue: 0.1364 time to fit residues: 2.8380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 4.9990 chunk 38 optimal weight: 20.0000 chunk 25 optimal weight: 0.4980 chunk 82 optimal weight: 0.0050 chunk 87 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 ASN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN B 673 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11394 Z= 0.208 Angle : 0.516 6.890 15472 Z= 0.274 Chirality : 0.043 0.163 1732 Planarity : 0.003 0.044 1920 Dihedral : 8.522 87.608 1570 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.82 % Allowed : 14.74 % Favored : 83.44 % 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: 604 sheet: 1.61 (0.28), residues: 286 loop : -1.72 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 629 HIS 0.004 0.001 HIS B 594 PHE 0.014 0.001 PHE B 632 TYR 0.014 0.001 TYR A 188 ARG 0.008 0.000 ARG A 821 *********************** 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 157 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 150 average time/residue: 1.0714 time to fit residues: 176.7734 Evaluate side-chains 145 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 132 time to evaluate : 1.210 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 2 average time/residue: 0.1519 time to fit residues: 2.1583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 20.0000 chunk 123 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 79 optimal weight: 0.4980 chunk 127 optimal weight: 5.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN A 691 ASN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN B 158 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 11394 Z= 0.376 Angle : 0.591 6.371 15472 Z= 0.313 Chirality : 0.046 0.209 1732 Planarity : 0.004 0.051 1920 Dihedral : 8.876 87.502 1570 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.57 % Allowed : 15.07 % Favored : 83.36 % 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: 0.59 (0.22), residues: 1348 helix: 1.29 (0.21), residues: 600 sheet: 1.63 (0.28), residues: 282 loop : -1.66 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 629 HIS 0.004 0.001 HIS B 229 PHE 0.017 0.002 PHE B 632 TYR 0.016 0.002 TYR B 759 ARG 0.004 0.000 ARG B 44 *********************** 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 157 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 1.258 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 15 residues processed: 151 average time/residue: 1.0860 time to fit residues: 180.0040 Evaluate side-chains 149 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 1.388 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 3 average time/residue: 0.1567 time to fit residues: 2.5149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN A 691 ASN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN B 673 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 11394 Z= 0.191 Angle : 0.518 6.626 15472 Z= 0.275 Chirality : 0.042 0.154 1732 Planarity : 0.003 0.036 1920 Dihedral : 8.595 88.430 1570 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.24 % Allowed : 15.48 % Favored : 83.28 % 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: 0.65 (0.23), residues: 1348 helix: 1.45 (0.21), residues: 602 sheet: 1.54 (0.28), residues: 282 loop : -1.72 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 629 HIS 0.007 0.001 HIS B 594 PHE 0.014 0.001 PHE B 632 TYR 0.013 0.001 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 150 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 1.287 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 14 residues processed: 147 average time/residue: 1.0998 time to fit residues: 177.1035 Evaluate side-chains 147 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 133 time to evaluate : 1.167 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 3 average time/residue: 0.5724 time to fit residues: 3.6715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 29 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 109 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 HIS A 691 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.158730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.109066 restraints weight = 12829.170| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.23 r_work: 0.3392 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11394 Z= 0.203 Angle : 0.513 6.506 15472 Z= 0.272 Chirality : 0.043 0.211 1732 Planarity : 0.003 0.034 1920 Dihedral : 8.428 88.406 1570 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.24 % Allowed : 15.56 % Favored : 83.20 % 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: 0.75 (0.23), residues: 1348 helix: 1.50 (0.21), residues: 602 sheet: 1.59 (0.28), residues: 286 loop : -1.66 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 629 HIS 0.006 0.001 HIS B 594 PHE 0.015 0.001 PHE B 621 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: 3969.90 seconds wall clock time: 74 minutes 33.75 seconds (4473.75 seconds total)