Starting phenix.real_space_refine on Sat Jul 20 15:56:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jun_36662/07_2024/8jun_36662_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jun_36662/07_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_36662/07_2024/8jun_36662.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jun_36662/07_2024/8jun_36662.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jun_36662/07_2024/8jun_36662_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jun_36662/07_2024/8jun_36662_neut.cif" } 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-5388/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: 6.71, per 1000 atoms: 0.60 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: 4.63 Conformation dependent library (CDL) restraints added in 2.2 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... Secondary structure from input PDB file: 38 helices and 10 sheets defined 47.6% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 268 through 272 Processing helix chain 'A' and resid 302 through 332 removed outlier: 3.637A pdb=" N TYR A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) 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 441 through 470 removed outlier: 3.585A pdb=" N PHE A 445 " --> pdb=" O TYR A 441 " (cutoff:3.500A) 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) removed outlier: 3.928A pdb=" N VAL A 470 " --> pdb=" O TYR A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 500 removed outlier: 3.750A pdb=" N ILE A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 528 removed outlier: 3.845A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 535 removed outlier: 3.699A pdb=" N VAL A 534 " --> pdb=" O ASP A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 565 removed outlier: 3.782A pdb=" N ALA A 547 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N CYS A 565 " --> pdb=" O CYS A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 575 Processing helix chain 'A' and resid 576 through 592 removed outlier: 3.839A pdb=" N MET A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 621 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 625 through 647 removed outlier: 3.691A pdb=" N ILE A 631 " --> pdb=" O TRP A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 668 removed outlier: 4.631A pdb=" N PHE A 667 " --> pdb=" O ALA A 663 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR A 668 " --> pdb=" O ALA A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 705 removed outlier: 4.264A pdb=" N MET A 684 " --> pdb=" O TYR A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 735 Processing helix chain 'A' and resid 740 through 762 Processing helix chain 'A' and resid 771 through 777 Processing helix chain 'A' and resid 789 through 812 Processing helix chain 'A' and resid 813 through 816 Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 268 through 272 Processing helix chain 'B' and resid 302 through 332 removed outlier: 3.637A pdb=" N TYR B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) 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 441 through 470 removed outlier: 3.585A pdb=" N PHE B 445 " --> pdb=" O TYR B 441 " (cutoff:3.500A) 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) removed outlier: 3.928A pdb=" N VAL B 470 " --> pdb=" O TYR B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 500 removed outlier: 3.749A pdb=" N ILE B 498 " --> pdb=" O ALA B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 528 removed outlier: 3.846A pdb=" N VAL B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 535 removed outlier: 3.699A pdb=" N VAL B 534 " --> pdb=" O ASP B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 565 removed outlier: 3.783A pdb=" N ALA B 547 " --> pdb=" O GLY B 543 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N CYS B 565 " --> pdb=" O CYS B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 575 Processing helix chain 'B' and resid 576 through 592 removed outlier: 3.840A pdb=" N MET B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 621 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 625 through 647 removed outlier: 3.691A pdb=" N ILE B 631 " --> pdb=" O TRP B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 668 removed outlier: 4.631A pdb=" N PHE B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR B 668 " --> pdb=" O ALA B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 705 removed outlier: 4.264A pdb=" N MET B 684 " --> pdb=" O TYR B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 735 Processing helix chain 'B' and resid 740 through 762 Processing helix chain 'B' and resid 771 through 777 Processing helix chain 'B' and resid 789 through 812 Processing helix chain 'B' and resid 813 through 816 Processing sheet with id=AA1, 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=AA2, first strand: chain 'A' and resid 62 through 70 Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 113 Processing sheet with id=AA4, first strand: chain 'A' and resid 177 through 181 Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 192 Processing sheet with id=AA6, 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=AA7, first strand: chain 'B' and resid 62 through 70 Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 113 Processing sheet with id=AA9, first strand: chain 'B' and resid 177 through 181 Processing sheet with id=AB1, first strand: chain 'B' and resid 187 through 192 614 hydrogen bonds defined for protein. 1746 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: 3.88 Time building geometry restraints manager: 5.11 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: 9023 3.15 - 3.73: 17013 3.73 - 4.32: 25671 4.32 - 4.90: 41145 Nonbonded interactions: 92906 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 92901 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: 0.990 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: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 36.540 Find NCS groups from input model: 0.450 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: 0.010 Load rotamer database and sin/cos tables:17.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.730 ------------------------------------------------------------------------------- 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= 0.443 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 : 1.206 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: 1.0809 time to fit residues: 227.3250 Evaluate side-chains 144 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 143 time to evaluate : 1.213 ------------------------------------------------------------------------------- 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: 5.9990 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 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: 1.5386 ------------------------------------------------------------------------------- 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: 0.7907 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 11394 Z= 0.270 Angle : 0.567 7.431 15472 Z= 0.306 Chirality : 0.044 0.166 1732 Planarity : 0.004 0.035 1920 Dihedral : 9.681 88.049 1572 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.66 % Allowed : 9.27 % Favored : 89.07 % 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: 0.65 (0.21), residues: 602 sheet: 1.18 (0.28), residues: 278 loop : -2.06 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 629 HIS 0.004 0.001 HIS B 229 PHE 0.014 0.002 PHE B 445 TYR 0.017 0.002 TYR B 680 ARG 0.012 0.001 ARG A 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 172 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 152 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6313 (mmm-85) cc_final: 0.5748 (ttm170) REVERT: A 145 ILE cc_start: 0.9039 (mt) cc_final: 0.8797 (mp) REVERT: A 536 TYR cc_start: 0.7318 (m-80) cc_final: 0.6905 (m-80) REVERT: A 650 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.6591 (mtt) REVERT: B 83 ASN cc_start: 0.7728 (p0) cc_final: 0.7411 (p0) REVERT: B 115 LEU cc_start: 0.8473 (mt) cc_final: 0.8267 (mt) REVERT: B 240 MET cc_start: 0.9204 (ttt) cc_final: 0.8894 (ttt) REVERT: B 536 TYR cc_start: 0.7908 (m-80) cc_final: 0.7583 (m-80) REVERT: B 548 MET cc_start: 0.8490 (mtt) cc_final: 0.8206 (mtp) REVERT: B 617 LEU cc_start: 0.7784 (mt) cc_final: 0.7513 (mm) REVERT: B 621 PHE cc_start: 0.8478 (m-80) cc_final: 0.8191 (m-80) REVERT: B 652 ARG cc_start: 0.6557 (mmt180) cc_final: 0.5485 (mtm180) REVERT: B 738 LYS cc_start: 0.8248 (ptpp) cc_final: 0.7948 (mtpp) outliers start: 20 outliers final: 7 residues processed: 162 average time/residue: 1.0253 time to fit residues: 182.4647 Evaluate side-chains 144 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 821 ARG 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 818 VAL 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: 2.9990 chunk 101 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 113 GLN B 497 ASN B 541 HIS B 624 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 11394 Z= 0.476 Angle : 0.665 6.505 15472 Z= 0.353 Chirality : 0.049 0.240 1732 Planarity : 0.004 0.052 1920 Dihedral : 9.491 91.876 1570 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.65 % Allowed : 10.93 % Favored : 86.42 % 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: 0.03 (0.22), residues: 1348 helix: 0.77 (0.21), residues: 610 sheet: 1.35 (0.28), residues: 282 loop : -1.93 (0.27), residues: 456 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 0.018 0.002 PHE B 253 TYR 0.021 0.002 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 184 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 152 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6228 (mmm-85) cc_final: 0.5754 (ttp-170) REVERT: A 63 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.7985 (tp) REVERT: A 90 ASN cc_start: 0.8036 (m-40) cc_final: 0.7740 (m-40) REVERT: A 143 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8006 (mt0) REVERT: A 145 ILE cc_start: 0.9056 (mt) cc_final: 0.8799 (mp) REVERT: A 274 SER cc_start: 0.7481 (OUTLIER) cc_final: 0.7179 (t) REVERT: A 536 TYR cc_start: 0.7477 (m-80) cc_final: 0.6925 (m-80) REVERT: A 540 LYS cc_start: 0.8225 (mttm) cc_final: 0.7915 (mmtt) REVERT: A 650 MET cc_start: 0.7070 (mtt) cc_final: 0.6449 (mtp) REVERT: A 707 ARG cc_start: 0.7895 (tpt-90) cc_final: 0.7490 (mtp180) REVERT: B 221 MET cc_start: 0.7074 (mtp) cc_final: 0.6738 (mpt) REVERT: B 446 TRP cc_start: 0.5984 (OUTLIER) cc_final: 0.5429 (m100) REVERT: B 536 TYR cc_start: 0.7825 (m-80) cc_final: 0.7597 (m-80) REVERT: B 617 LEU cc_start: 0.7777 (mt) cc_final: 0.7518 (mm) REVERT: B 621 PHE cc_start: 0.8613 (m-80) cc_final: 0.8236 (m-80) REVERT: B 623 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7789 (mmtm) REVERT: B 650 MET cc_start: 0.6857 (OUTLIER) cc_final: 0.6332 (mtt) REVERT: B 652 ARG cc_start: 0.7032 (mmt180) cc_final: 0.5823 (mtt180) REVERT: B 704 TYR cc_start: 0.7769 (m-80) cc_final: 0.7472 (m-80) outliers start: 32 outliers final: 15 residues processed: 170 average time/residue: 1.0562 time to fit residues: 196.6800 Evaluate side-chains 162 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 1.331 ------------------------------------------------------------------------------- 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 260 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 607 SER 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 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 623 LYS Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 696 SER 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: 20.0000 chunk 91 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 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 229 HIS A 447 ASN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11394 Z= 0.176 Angle : 0.499 5.946 15472 Z= 0.268 Chirality : 0.042 0.140 1732 Planarity : 0.003 0.035 1920 Dihedral : 8.732 84.339 1570 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.81 % Allowed : 11.51 % Favored : 85.68 % 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: 0.45 (0.23), residues: 1348 helix: 1.33 (0.21), residues: 606 sheet: 1.42 (0.29), residues: 282 loop : -1.92 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 629 HIS 0.004 0.001 HIS B 594 PHE 0.010 0.001 PHE B 632 TYR 0.013 0.001 TYR A 210 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 179 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 145 time to evaluate : 1.227 Fit side-chains revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6212 (mmm-85) cc_final: 0.5991 (ttp-170) REVERT: A 63 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.7864 (tp) REVERT: A 90 ASN cc_start: 0.7920 (m-40) cc_final: 0.7648 (m-40) REVERT: A 143 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.7973 (mt0) REVERT: A 145 ILE cc_start: 0.9019 (mt) cc_final: 0.8769 (mp) REVERT: A 536 TYR cc_start: 0.7443 (m-80) cc_final: 0.7095 (m-80) REVERT: A 540 LYS cc_start: 0.8127 (mttm) cc_final: 0.7884 (mmtt) REVERT: A 554 MET cc_start: 0.7373 (tpp) cc_final: 0.7052 (mmt) REVERT: A 602 TYR cc_start: 0.4266 (OUTLIER) cc_final: 0.3056 (m-80) REVERT: A 707 ARG cc_start: 0.7773 (tpt-90) cc_final: 0.7358 (mtp180) REVERT: B 71 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7572 (mp-120) REVERT: B 83 ASN cc_start: 0.7695 (p0) cc_final: 0.7435 (p0) REVERT: B 446 TRP cc_start: 0.6065 (OUTLIER) cc_final: 0.5459 (m100) REVERT: B 536 TYR cc_start: 0.7718 (m-80) cc_final: 0.7412 (m-80) REVERT: B 621 PHE cc_start: 0.8531 (m-80) cc_final: 0.8236 (m-80) REVERT: B 652 ARG cc_start: 0.6914 (mmt180) cc_final: 0.5761 (mtm110) outliers start: 34 outliers final: 12 residues processed: 162 average time/residue: 1.0219 time to fit residues: 181.7040 Evaluate side-chains 152 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 136 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 260 VAL Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 645 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 446 TRP 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 696 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 3.9990 chunk 1 optimal weight: 0.0870 chunk 96 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 32 optimal weight: 0.0170 chunk 43 optimal weight: 1.9990 overall best weight: 1.2202 ------------------------------------------------------------------------------- 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 447 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11394 Z= 0.219 Angle : 0.527 10.796 15472 Z= 0.280 Chirality : 0.043 0.152 1732 Planarity : 0.003 0.034 1920 Dihedral : 8.758 84.020 1570 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.40 % Allowed : 12.42 % Favored : 85.18 % 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: 0.56 (0.23), residues: 1348 helix: 1.35 (0.21), residues: 612 sheet: 1.49 (0.28), residues: 286 loop : -1.82 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 629 HIS 0.003 0.001 HIS B 594 PHE 0.014 0.001 PHE B 632 TYR 0.013 0.002 TYR A 188 ARG 0.003 0.000 ARG A 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: 29 poor density : 144 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6215 (mmm-85) cc_final: 0.6005 (ttp-170) REVERT: A 63 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.7819 (tp) REVERT: A 90 ASN cc_start: 0.7964 (m-40) cc_final: 0.7687 (m-40) REVERT: A 143 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7967 (mt0) REVERT: A 145 ILE cc_start: 0.9027 (mt) cc_final: 0.8778 (mp) REVERT: A 536 TYR cc_start: 0.7434 (m-80) cc_final: 0.6994 (m-80) REVERT: A 540 LYS cc_start: 0.8167 (mttm) cc_final: 0.7913 (mmtt) REVERT: A 554 MET cc_start: 0.7390 (tpp) cc_final: 0.7092 (mmt) REVERT: A 602 TYR cc_start: 0.4406 (OUTLIER) cc_final: 0.3120 (m-80) REVERT: A 707 ARG cc_start: 0.7790 (tpt-90) cc_final: 0.7408 (mtp180) REVERT: B 83 ASN cc_start: 0.7659 (p0) cc_final: 0.7334 (p0) REVERT: B 446 TRP cc_start: 0.6065 (OUTLIER) cc_final: 0.5456 (m100) REVERT: B 536 TYR cc_start: 0.7680 (m-80) cc_final: 0.7442 (m-80) REVERT: B 621 PHE cc_start: 0.8529 (m-80) cc_final: 0.8243 (m-80) REVERT: B 666 VAL cc_start: 0.5998 (OUTLIER) cc_final: 0.5788 (t) outliers start: 29 outliers final: 18 residues processed: 162 average time/residue: 0.9825 time to fit residues: 175.6262 Evaluate side-chains 158 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 1.311 ------------------------------------------------------------------------------- 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 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 124 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 446 TRP 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 623 LYS Chi-restraints excluded: chain B residue 666 VAL 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: 8.9990 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 chunk 124 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 673 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11394 Z= 0.299 Angle : 0.556 6.008 15472 Z= 0.297 Chirality : 0.044 0.182 1732 Planarity : 0.004 0.040 1920 Dihedral : 8.667 85.985 1570 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.57 % Allowed : 12.33 % 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: 0.56 (0.23), residues: 1348 helix: 1.26 (0.21), residues: 612 sheet: 1.57 (0.28), residues: 282 loop : -1.71 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 629 HIS 0.003 0.001 HIS B 594 PHE 0.017 0.002 PHE B 632 TYR 0.015 0.002 TYR B 759 ARG 0.006 0.000 ARG B 118 *********************** 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 173 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 142 time to evaluate : 1.108 Fit side-chains revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.7876 (tp) REVERT: A 90 ASN cc_start: 0.8006 (m-40) cc_final: 0.7743 (m-40) REVERT: A 143 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.7969 (mt0) REVERT: A 145 ILE cc_start: 0.9044 (mt) cc_final: 0.8794 (mp) REVERT: A 536 TYR cc_start: 0.7526 (m-80) cc_final: 0.7215 (m-80) REVERT: A 540 LYS cc_start: 0.8212 (mttm) cc_final: 0.7963 (mmmt) REVERT: A 554 MET cc_start: 0.7381 (tpp) cc_final: 0.7111 (mmt) REVERT: A 602 TYR cc_start: 0.4254 (OUTLIER) cc_final: 0.3101 (m-80) REVERT: A 613 MET cc_start: 0.7153 (tpt) cc_final: 0.6769 (mmm) REVERT: A 681 MET cc_start: 0.5177 (OUTLIER) cc_final: 0.4937 (ttp) REVERT: A 707 ARG cc_start: 0.7797 (tpt-90) cc_final: 0.7386 (mtp180) REVERT: B 71 GLN cc_start: 0.8000 (mm-40) cc_final: 0.7566 (mp-120) REVERT: B 276 PHE cc_start: 0.5894 (OUTLIER) cc_final: 0.4952 (t80) REVERT: B 446 TRP cc_start: 0.6114 (OUTLIER) cc_final: 0.5510 (m100) REVERT: B 447 ASN cc_start: 0.6893 (m-40) cc_final: 0.6648 (m-40) REVERT: B 536 TYR cc_start: 0.7636 (m-80) cc_final: 0.7317 (m-80) REVERT: B 621 PHE cc_start: 0.8581 (m-80) cc_final: 0.8271 (m-80) outliers start: 31 outliers final: 19 residues processed: 163 average time/residue: 1.0039 time to fit residues: 180.0871 Evaluate side-chains 158 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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 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 681 MET 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 449 ILE Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 822 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 673 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11394 Z= 0.188 Angle : 0.509 10.458 15472 Z= 0.270 Chirality : 0.042 0.155 1732 Planarity : 0.003 0.035 1920 Dihedral : 8.532 84.913 1570 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.81 % Allowed : 12.75 % Favored : 84.44 % 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: 0.67 (0.23), residues: 1348 helix: 1.40 (0.21), residues: 614 sheet: 1.54 (0.28), residues: 282 loop : -1.68 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 629 HIS 0.003 0.001 HIS B 594 PHE 0.014 0.001 PHE B 632 TYR 0.013 0.001 TYR A 188 ARG 0.005 0.000 ARG B 118 *********************** 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 172 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 138 time to evaluate : 1.172 Fit side-chains revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8359 (mm) cc_final: 0.7824 (tp) REVERT: A 90 ASN cc_start: 0.7981 (m-40) cc_final: 0.7724 (m-40) REVERT: A 143 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.7983 (mt0) REVERT: A 145 ILE cc_start: 0.9023 (mt) cc_final: 0.8775 (mp) REVERT: A 536 TYR cc_start: 0.7486 (m-80) cc_final: 0.7224 (m-80) REVERT: A 540 LYS cc_start: 0.8167 (mttm) cc_final: 0.7912 (mmtt) REVERT: A 554 MET cc_start: 0.7313 (tpp) cc_final: 0.7054 (mmt) REVERT: A 602 TYR cc_start: 0.4314 (OUTLIER) cc_final: 0.3229 (m-80) REVERT: A 613 MET cc_start: 0.7159 (tpt) cc_final: 0.6808 (mmm) REVERT: A 707 ARG cc_start: 0.7762 (tpt-90) cc_final: 0.7403 (mtp180) REVERT: B 83 ASN cc_start: 0.7730 (p0) cc_final: 0.7460 (p0) REVERT: B 276 PHE cc_start: 0.5705 (OUTLIER) cc_final: 0.4763 (t80) REVERT: B 446 TRP cc_start: 0.6072 (OUTLIER) cc_final: 0.5486 (m100) REVERT: B 536 TYR cc_start: 0.7528 (m-80) cc_final: 0.7292 (m-80) REVERT: B 621 PHE cc_start: 0.8553 (m-80) cc_final: 0.8295 (m-80) outliers start: 34 outliers final: 17 residues processed: 162 average time/residue: 0.9672 time to fit residues: 173.0085 Evaluate side-chains 156 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 135 time to evaluate : 1.427 ------------------------------------------------------------------------------- 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 143 GLN 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 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 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 623 LYS Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 692 LEU 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: 4.9990 chunk 38 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 87 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 112 optimal weight: 20.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 447 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11394 Z= 0.171 Angle : 0.495 6.247 15472 Z= 0.264 Chirality : 0.042 0.146 1732 Planarity : 0.003 0.033 1920 Dihedral : 8.361 86.021 1570 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.48 % Allowed : 13.16 % Favored : 84.35 % 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: 0.80 (0.23), residues: 1348 helix: 1.51 (0.21), residues: 614 sheet: 1.58 (0.28), residues: 282 loop : -1.60 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 629 HIS 0.004 0.001 HIS B 594 PHE 0.013 0.001 PHE B 632 TYR 0.013 0.001 TYR A 188 ARG 0.005 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 168 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 138 time to evaluate : 1.275 Fit side-chains revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.7775 (tp) REVERT: A 90 ASN cc_start: 0.7963 (m-40) cc_final: 0.7721 (m-40) REVERT: A 143 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.7947 (mt0) REVERT: A 145 ILE cc_start: 0.9026 (mt) cc_final: 0.8783 (mp) REVERT: A 536 TYR cc_start: 0.7539 (m-80) cc_final: 0.7260 (m-80) REVERT: A 540 LYS cc_start: 0.8092 (mttm) cc_final: 0.7864 (mmtt) REVERT: A 554 MET cc_start: 0.7194 (tpp) cc_final: 0.6966 (mmt) REVERT: A 602 TYR cc_start: 0.4430 (OUTLIER) cc_final: 0.3508 (m-80) REVERT: A 613 MET cc_start: 0.7171 (tpt) cc_final: 0.6861 (mmm) REVERT: A 707 ARG cc_start: 0.7737 (tpt-90) cc_final: 0.7338 (mtp180) REVERT: B 58 LEU cc_start: 0.9145 (tp) cc_final: 0.8886 (tm) REVERT: B 71 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7654 (mp-120) REVERT: B 83 ASN cc_start: 0.7641 (p0) cc_final: 0.7398 (p0) REVERT: B 276 PHE cc_start: 0.5659 (OUTLIER) cc_final: 0.4750 (t80) REVERT: B 536 TYR cc_start: 0.7468 (m-80) cc_final: 0.7233 (m-80) REVERT: B 621 PHE cc_start: 0.8546 (m-80) cc_final: 0.8314 (m-80) REVERT: B 699 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7667 (tm) outliers start: 30 outliers final: 18 residues processed: 159 average time/residue: 1.0146 time to fit residues: 178.0304 Evaluate side-chains 151 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 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 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 623 LYS Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 703 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.4980 chunk 123 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 0.0040 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 119 optimal weight: 0.3980 chunk 79 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3307 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= 0.211 Angle : 0.513 5.843 15472 Z= 0.272 Chirality : 0.043 0.160 1732 Planarity : 0.003 0.034 1920 Dihedral : 8.421 85.061 1570 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.15 % Allowed : 13.41 % Favored : 84.44 % 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: 0.86 (0.23), residues: 1348 helix: 1.53 (0.21), residues: 612 sheet: 1.62 (0.28), residues: 286 loop : -1.54 (0.28), residues: 450 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 0.014 0.001 PHE B 632 TYR 0.014 0.001 TYR A 188 ARG 0.004 0.000 ARG A 821 *********************** 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 160 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 1.230 Fit side-chains revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.7766 (tp) REVERT: A 90 ASN cc_start: 0.8003 (m-40) cc_final: 0.7746 (m-40) REVERT: A 145 ILE cc_start: 0.9036 (mt) cc_final: 0.8785 (mp) REVERT: A 536 TYR cc_start: 0.7643 (m-80) cc_final: 0.7372 (m-80) REVERT: A 554 MET cc_start: 0.7228 (tpp) cc_final: 0.6975 (mmt) REVERT: A 602 TYR cc_start: 0.4331 (OUTLIER) cc_final: 0.3266 (m-80) REVERT: A 613 MET cc_start: 0.7156 (tpt) cc_final: 0.6799 (mmm) REVERT: A 625 ASP cc_start: 0.6856 (t0) cc_final: 0.6617 (t0) REVERT: A 707 ARG cc_start: 0.7758 (tpt-90) cc_final: 0.7419 (mtp180) REVERT: B 71 GLN cc_start: 0.8065 (mm-40) cc_final: 0.7600 (mp-120) REVERT: B 83 ASN cc_start: 0.7750 (p0) cc_final: 0.7444 (p0) REVERT: B 276 PHE cc_start: 0.5742 (OUTLIER) cc_final: 0.4731 (t80) REVERT: B 446 TRP cc_start: 0.6056 (OUTLIER) cc_final: 0.5506 (m100) REVERT: B 447 ASN cc_start: 0.6955 (m-40) cc_final: 0.6677 (m-40) REVERT: B 536 TYR cc_start: 0.7452 (m-80) cc_final: 0.7216 (m-80) REVERT: B 621 PHE cc_start: 0.8564 (m-80) cc_final: 0.8295 (m-80) REVERT: B 699 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7611 (tm) outliers start: 26 outliers final: 19 residues processed: 154 average time/residue: 0.9090 time to fit residues: 155.1684 Evaluate side-chains 156 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 1.174 ------------------------------------------------------------------------------- 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 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 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 623 LYS Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain B residue 822 ASP 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: 2.9990 chunk 88 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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: 0.7931 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11394 Z= 0.319 Angle : 0.576 7.043 15472 Z= 0.306 Chirality : 0.045 0.188 1732 Planarity : 0.004 0.041 1920 Dihedral : 8.823 85.445 1570 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.90 % Allowed : 13.58 % 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: 0.73 (0.23), residues: 1348 helix: 1.34 (0.21), residues: 612 sheet: 1.65 (0.28), residues: 282 loop : -1.52 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 629 HIS 0.003 0.001 HIS B 229 PHE 0.019 0.002 PHE B 632 TYR 0.016 0.002 TYR B 759 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 158 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 1.208 Fit side-chains revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7595 (tp) REVERT: A 90 ASN cc_start: 0.8006 (m-40) cc_final: 0.7759 (m-40) REVERT: A 145 ILE cc_start: 0.9053 (mt) cc_final: 0.8804 (mp) REVERT: A 536 TYR cc_start: 0.7674 (m-80) cc_final: 0.7435 (m-80) REVERT: A 554 MET cc_start: 0.7335 (tpp) cc_final: 0.7050 (mmt) REVERT: A 602 TYR cc_start: 0.4403 (OUTLIER) cc_final: 0.3262 (m-80) REVERT: A 613 MET cc_start: 0.7139 (tpt) cc_final: 0.6760 (mmm) REVERT: A 707 ARG cc_start: 0.7794 (tpt-90) cc_final: 0.7453 (mtp180) REVERT: B 276 PHE cc_start: 0.5912 (OUTLIER) cc_final: 0.4967 (t80) REVERT: B 446 TRP cc_start: 0.6064 (OUTLIER) cc_final: 0.5517 (m100) REVERT: B 447 ASN cc_start: 0.7035 (m-40) cc_final: 0.6782 (m-40) REVERT: B 536 TYR cc_start: 0.7439 (m-80) cc_final: 0.7166 (m-80) REVERT: B 621 PHE cc_start: 0.8422 (m-80) cc_final: 0.8150 (m-80) outliers start: 23 outliers final: 15 residues processed: 154 average time/residue: 1.0057 time to fit residues: 170.8232 Evaluate side-chains 145 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 126 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 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 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 666 VAL Chi-restraints excluded: chain B residue 696 SER Chi-restraints excluded: chain B residue 703 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 106 optimal weight: 0.4980 chunk 44 optimal weight: 0.0370 chunk 109 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.159628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.111491 restraints weight = 12883.410| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.18 r_work: 0.3403 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11394 Z= 0.156 Angle : 0.500 8.767 15472 Z= 0.263 Chirality : 0.042 0.194 1732 Planarity : 0.003 0.034 1920 Dihedral : 8.417 87.792 1570 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.32 % Allowed : 14.57 % Favored : 84.11 % 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: 0.89 (0.23), residues: 1348 helix: 1.54 (0.21), residues: 616 sheet: 1.61 (0.29), residues: 282 loop : -1.48 (0.28), residues: 450 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 0.012 0.001 TYR A 188 ARG 0.005 0.000 ARG A 705 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4016.16 seconds wall clock time: 71 minutes 8.26 seconds (4268.26 seconds total)