Starting phenix.real_space_refine on Mon Mar 11 13:55:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozu_13135/03_2024/7ozu_13135_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozu_13135/03_2024/7ozu_13135.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozu_13135/03_2024/7ozu_13135_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozu_13135/03_2024/7ozu_13135_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozu_13135/03_2024/7ozu_13135_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozu_13135/03_2024/7ozu_13135.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozu_13135/03_2024/7ozu_13135.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozu_13135/03_2024/7ozu_13135_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozu_13135/03_2024/7ozu_13135_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 22 5.49 5 S 57 5.16 5 C 5284 2.51 5 N 1405 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 865": "OD1" <-> "OD2" Residue "A TYR 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 155": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8408 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 6565 Classifications: {'peptide': 814} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 786} Chain breaks: 3 Chain: "B" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 109} Chain: "C" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 478 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "P" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 212 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 260 Classifications: {'RNA': 12} Modifications used: {'rna3p': 1, 'rna3p_pur': 7, 'rna3p_pyr': 4} Link IDs: {'rna3p': 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1692 SG CYS A 301 47.629 66.446 35.948 1.00 75.77 S ATOM 1733 SG CYS A 306 47.619 65.877 32.167 1.00 71.14 S ATOM 1765 SG CYS A 310 50.645 65.595 34.602 1.00 65.59 S ATOM 3132 SG CYS A 487 29.807 62.600 44.981 1.00 68.93 S ATOM 4385 SG CYS A 645 28.884 62.549 41.352 1.00 75.15 S ATOM 4391 SG CYS A 646 31.664 64.707 42.888 1.00 71.21 S Time building chain proxies: 5.20, per 1000 atoms: 0.62 Number of scatterers: 8408 At special positions: 0 Unit cell: (90.906, 94.242, 98.412, 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 57 16.00 P 22 15.00 O 1638 8.00 N 1405 7.00 C 5284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.32 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 306 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 310 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 301 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 487 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 646 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 645 " pdb="ZN ZN A2001 " - pdb=" ND1 HIS A 642 " Number of angles added : 6 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1898 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 7 sheets defined 48.0% alpha, 9.8% beta 7 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 4.19 Creating SS restraints... Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 154 through 158 removed outlier: 4.064A pdb=" N ASN A 158 " --> pdb=" O ASP A 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 158' Processing helix chain 'A' and resid 169 through 199 removed outlier: 4.074A pdb=" N TYR A 175 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 235 through 247 Proline residue: A 243 - end of helix removed outlier: 3.812A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 4.267A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 276 through 285 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 304 through 317 removed outlier: 3.693A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 378 through 384 removed outlier: 3.609A pdb=" N SER A 384 " --> pdb=" O MET A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.746A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 480 removed outlier: 3.726A pdb=" N LYS A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 521 through 531 Processing helix chain 'A' and resid 562 through 581 removed outlier: 5.757A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 Processing helix chain 'A' and resid 622 through 625 No H-bonds generated for 'chain 'A' and resid 622 through 625' Processing helix chain 'A' and resid 628 through 638 Processing helix chain 'A' and resid 648 through 661 Processing helix chain 'A' and resid 687 through 709 Processing helix chain 'A' and resid 718 through 731 Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 779 through 788 Processing helix chain 'A' and resid 796 through 798 No H-bonds generated for 'chain 'A' and resid 796 through 798' Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 847 through 850 Processing helix chain 'A' and resid 853 through 865 removed outlier: 3.869A pdb=" N GLU A 857 " --> pdb=" O THR A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 871 Processing helix chain 'A' and resid 875 through 895 removed outlier: 3.916A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 915 Processing helix chain 'A' and resid 918 through 925 removed outlier: 3.853A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TYR A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 97 Processing helix chain 'B' and resid 100 through 109 removed outlier: 4.042A pdb=" N ASN B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix removed outlier: 3.735A pdb=" N THR B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 142 Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'C' and resid 2 through 20 Processing helix chain 'C' and resid 22 through 24 No H-bonds generated for 'chain 'C' and resid 22 through 24' Processing helix chain 'C' and resid 26 through 41 Processing helix chain 'C' and resid 45 through 61 Processing sheet with id= A, first strand: chain 'A' and resid 32 through 38 Processing sheet with id= B, first strand: chain 'A' and resid 330 through 335 Processing sheet with id= C, first strand: chain 'A' and resid 345 through 348 Processing sheet with id= D, first strand: chain 'A' and resid 556 through 559 removed outlier: 5.938A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N MET A 542 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N MET A 668 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 800 through 802 removed outlier: 4.120A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 816 through 822 Processing sheet with id= G, first strand: chain 'B' and resid 127 through 132 removed outlier: 6.061A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 879 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 18 hydrogen bonds 36 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 3.17 Time building geometry restraints manager: 4.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1330 1.31 - 1.43: 2520 1.43 - 1.56: 4659 1.56 - 1.68: 46 1.68 - 1.81: 87 Bond restraints: 8642 Sorted by residual: bond pdb=" O4' 7OK T 9 " pdb=" C1' 7OK T 9 " ideal model delta sigma weight residual 1.412 1.626 -0.214 1.50e-02 4.44e+03 2.03e+02 bond pdb=" C2' 7OK T 9 " pdb=" C1' 7OK T 9 " ideal model delta sigma weight residual 1.529 1.346 0.183 1.50e-02 4.44e+03 1.50e+02 bond pdb=" C4' 7OK T 9 " pdb=" O4' 7OK T 9 " ideal model delta sigma weight residual 1.451 1.299 0.152 1.50e-02 4.44e+03 1.03e+02 bond pdb=" C4 7OK T 9 " pdb=" N4 7OK T 9 " ideal model delta sigma weight residual 1.261 1.439 -0.178 2.00e-02 2.50e+03 7.96e+01 bond pdb=" C2 7OK T 9 " pdb=" N3 7OK T 9 " ideal model delta sigma weight residual 1.494 1.329 0.165 2.00e-02 2.50e+03 6.77e+01 ... (remaining 8637 not shown) Histogram of bond angle deviations from ideal: 92.05 - 100.44: 7 100.44 - 108.83: 635 108.83 - 117.22: 5515 117.22 - 125.60: 5493 125.60 - 133.99: 181 Bond angle restraints: 11831 Sorted by residual: angle pdb=" O3' 7OK T 9 " pdb=" P A T 10 " pdb=" O5' A T 10 " ideal model delta sigma weight residual 104.00 92.05 11.95 1.50e+00 4.44e-01 6.34e+01 angle pdb=" C2' 7OK T 9 " pdb=" C1' 7OK T 9 " pdb=" N1 7OK T 9 " ideal model delta sigma weight residual 112.00 122.08 -10.08 1.50e+00 4.44e-01 4.52e+01 angle pdb=" O4' 7OK T 9 " pdb=" C1' 7OK T 9 " pdb=" N1 7OK T 9 " ideal model delta sigma weight residual 108.50 100.57 7.93 1.50e+00 4.44e-01 2.79e+01 angle pdb=" O3' 7OK T 9 " pdb=" P A T 10 " pdb=" OP2 A T 10 " ideal model delta sigma weight residual 108.00 119.56 -11.56 3.00e+00 1.11e-01 1.48e+01 angle pdb=" C5' 7OK T 9 " pdb=" C4' 7OK T 9 " pdb=" C3' 7OK T 9 " ideal model delta sigma weight residual 116.00 110.24 5.76 1.50e+00 4.44e-01 1.48e+01 ... (remaining 11826 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 4654 17.03 - 34.06: 382 34.06 - 51.09: 64 51.09 - 68.12: 42 68.12 - 85.15: 11 Dihedral angle restraints: 5153 sinusoidal: 2213 harmonic: 2940 Sorted by residual: dihedral pdb=" CA LEU A 758 " pdb=" C LEU A 758 " pdb=" N SER A 759 " pdb=" CA SER A 759 " ideal model delta harmonic sigma weight residual 180.00 159.43 20.57 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA PHE A 571 " pdb=" C PHE A 571 " pdb=" N HIS A 572 " pdb=" CA HIS A 572 " ideal model delta harmonic sigma weight residual 180.00 -162.96 -17.04 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA TRP A 290 " pdb=" C TRP A 290 " pdb=" N ASP A 291 " pdb=" CA ASP A 291 " ideal model delta harmonic sigma weight residual -180.00 -163.53 -16.47 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 5150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1268 0.084 - 0.168: 74 0.168 - 0.252: 0 0.252 - 0.336: 0 0.336 - 0.420: 1 Chirality restraints: 1343 Sorted by residual: chirality pdb=" C2' 7OK T 9 " pdb=" C3' 7OK T 9 " pdb=" O2' 7OK T 9 " pdb=" C1' 7OK T 9 " both_signs ideal model delta sigma weight residual False -2.75 -2.33 -0.42 2.00e-01 2.50e+01 4.41e+00 chirality pdb=" CA ASN A 138 " pdb=" N ASN A 138 " pdb=" C ASN A 138 " pdb=" CB ASN A 138 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA ILE A 757 " pdb=" N ILE A 757 " pdb=" C ILE A 757 " pdb=" CB ILE A 757 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.26e-01 ... (remaining 1340 not shown) Planarity restraints: 1425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 7OK T 9 " -0.081 2.00e-02 2.50e+03 1.18e-01 3.48e+02 pdb=" N1 7OK T 9 " -0.008 2.00e-02 2.50e+03 pdb=" C2 7OK T 9 " -0.016 2.00e-02 2.50e+03 pdb=" O2 7OK T 9 " -0.068 2.00e-02 2.50e+03 pdb=" N3 7OK T 9 " 0.040 2.00e-02 2.50e+03 pdb=" C4 7OK T 9 " 0.099 2.00e-02 2.50e+03 pdb=" N4 7OK T 9 " 0.160 2.00e-02 2.50e+03 pdb=" C5 7OK T 9 " 0.105 2.00e-02 2.50e+03 pdb=" C6 7OK T 9 " 0.048 2.00e-02 2.50e+03 pdb=" OAC 7OK T 9 " -0.278 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 926 " 0.042 5.00e-02 4.00e+02 6.54e-02 6.85e+00 pdb=" N PRO A 927 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 927 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 927 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 758 " -0.010 2.00e-02 2.50e+03 2.12e-02 4.50e+00 pdb=" C LEU A 758 " 0.037 2.00e-02 2.50e+03 pdb=" O LEU A 758 " -0.014 2.00e-02 2.50e+03 pdb=" N SER A 759 " -0.012 2.00e-02 2.50e+03 ... (remaining 1422 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1177 2.75 - 3.29: 8132 3.29 - 3.83: 14217 3.83 - 4.36: 17446 4.36 - 4.90: 29370 Nonbonded interactions: 70342 Sorted by model distance: nonbonded pdb=" OD2 ASP A 260 " pdb=" OG1 THR A 262 " model vdw 2.218 2.440 nonbonded pdb=" NZ LYS A 426 " pdb=" OE1 GLN A 886 " model vdw 2.220 2.520 nonbonded pdb=" OG SER A 343 " pdb=" OD2 ASP A 377 " model vdw 2.226 2.440 nonbonded pdb=" OG1 THR A 206 " pdb=" OD1 ASN A 209 " model vdw 2.234 2.440 nonbonded pdb=" OG SER A 318 " pdb=" O ARG A 349 " model vdw 2.241 2.440 ... (remaining 70337 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.830 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: 3.510 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 35.270 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 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 0.214 8642 Z= 0.427 Angle : 0.522 11.948 11831 Z= 0.284 Chirality : 0.041 0.420 1343 Planarity : 0.005 0.118 1425 Dihedral : 14.139 85.155 3255 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.39 (0.26), residues: 979 helix: 0.69 (0.25), residues: 459 sheet: -0.09 (0.52), residues: 96 loop : 0.02 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 916 HIS 0.006 0.001 HIS A 613 PHE 0.035 0.002 PHE A 368 TYR 0.010 0.001 TYR A 788 ARG 0.004 0.000 ARG A 285 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.904 Fit side-chains REVERT: A 144 GLU cc_start: 0.6970 (mp0) cc_final: 0.6570 (mp0) REVERT: A 153 ASP cc_start: 0.7325 (m-30) cc_final: 0.7075 (m-30) REVERT: A 155 ASP cc_start: 0.7889 (m-30) cc_final: 0.7645 (m-30) REVERT: A 438 LYS cc_start: 0.7247 (mtmm) cc_final: 0.7045 (mttm) REVERT: A 546 TYR cc_start: 0.7508 (t80) cc_final: 0.6911 (t80) REVERT: A 668 MET cc_start: 0.7818 (tpt) cc_final: 0.7250 (tpt) REVERT: B 173 SER cc_start: 0.7447 (m) cc_final: 0.6940 (p) REVERT: C 38 ASP cc_start: 0.6528 (m-30) cc_final: 0.6069 (m-30) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2657 time to fit residues: 42.2545 Evaluate side-chains 91 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN B 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8642 Z= 0.318 Angle : 0.522 6.226 11831 Z= 0.274 Chirality : 0.042 0.142 1343 Planarity : 0.004 0.043 1425 Dihedral : 11.633 73.679 1417 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.14 % Allowed : 7.88 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.33 (0.26), residues: 979 helix: 0.67 (0.24), residues: 459 sheet: -0.13 (0.51), residues: 96 loop : -0.05 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.007 0.001 HIS A 309 PHE 0.018 0.002 PHE A 741 TYR 0.011 0.001 TYR A 788 ARG 0.005 0.000 ARG A 533 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 1.053 Fit side-chains REVERT: A 153 ASP cc_start: 0.7356 (m-30) cc_final: 0.7079 (m-30) REVERT: A 155 ASP cc_start: 0.7896 (m-30) cc_final: 0.7681 (m-30) REVERT: A 368 PHE cc_start: 0.7640 (t80) cc_final: 0.7336 (t80) REVERT: A 438 LYS cc_start: 0.7312 (mtmm) cc_final: 0.7102 (mttm) REVERT: A 546 TYR cc_start: 0.7597 (t80) cc_final: 0.7017 (t80) REVERT: A 548 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7632 (mp) REVERT: A 890 LYS cc_start: 0.7519 (tttt) cc_final: 0.7224 (tttp) REVERT: B 173 SER cc_start: 0.7482 (m) cc_final: 0.6967 (p) REVERT: C 38 ASP cc_start: 0.6509 (m-30) cc_final: 0.6050 (m-30) outliers start: 10 outliers final: 5 residues processed: 100 average time/residue: 0.1975 time to fit residues: 28.0845 Evaluate side-chains 97 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain B residue 148 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 81 optimal weight: 0.1980 chunk 31 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8642 Z= 0.125 Angle : 0.410 5.662 11831 Z= 0.216 Chirality : 0.038 0.136 1343 Planarity : 0.003 0.041 1425 Dihedral : 11.534 73.477 1417 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.26 % Allowed : 10.50 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.74 (0.26), residues: 979 helix: 1.03 (0.25), residues: 459 sheet: 0.30 (0.57), residues: 85 loop : 0.08 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 PHE 0.014 0.001 PHE A 741 TYR 0.015 0.001 TYR A 453 ARG 0.004 0.000 ARG A 533 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 0.872 Fit side-chains REVERT: A 144 GLU cc_start: 0.6884 (mp0) cc_final: 0.6401 (mt-10) REVERT: A 153 ASP cc_start: 0.7304 (m-30) cc_final: 0.7009 (m-30) REVERT: A 155 ASP cc_start: 0.7834 (m-30) cc_final: 0.7612 (m-30) REVERT: A 160 LYS cc_start: 0.6445 (mmtm) cc_final: 0.5914 (ttmt) REVERT: A 438 LYS cc_start: 0.7222 (mtmm) cc_final: 0.7011 (mttm) REVERT: A 546 TYR cc_start: 0.7449 (t80) cc_final: 0.6881 (t80) REVERT: A 890 LYS cc_start: 0.7540 (tttt) cc_final: 0.7213 (tttp) REVERT: B 173 SER cc_start: 0.7448 (m) cc_final: 0.6897 (p) REVERT: C 38 ASP cc_start: 0.6521 (m-30) cc_final: 0.6101 (m-30) outliers start: 11 outliers final: 8 residues processed: 103 average time/residue: 0.1973 time to fit residues: 28.9339 Evaluate side-chains 99 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 6 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 43 optimal weight: 0.7980 chunk 61 optimal weight: 0.3980 chunk 91 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8642 Z= 0.277 Angle : 0.482 6.104 11831 Z= 0.253 Chirality : 0.040 0.146 1343 Planarity : 0.003 0.045 1425 Dihedral : 11.575 73.814 1417 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.94 % Allowed : 12.33 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 (0.26), residues: 979 helix: 0.91 (0.24), residues: 460 sheet: 0.23 (0.56), residues: 85 loop : 0.01 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.007 0.001 HIS A 309 PHE 0.017 0.002 PHE A 741 TYR 0.016 0.001 TYR A 289 ARG 0.002 0.000 ARG A 569 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 0.906 Fit side-chains REVERT: A 144 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6426 (mt-10) REVERT: A 153 ASP cc_start: 0.7297 (m-30) cc_final: 0.6992 (m-30) REVERT: A 155 ASP cc_start: 0.7864 (m-30) cc_final: 0.7647 (m-30) REVERT: A 160 LYS cc_start: 0.6485 (mmtm) cc_final: 0.5717 (pttm) REVERT: A 280 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6712 (mp) REVERT: A 377 ASP cc_start: 0.8366 (t0) cc_final: 0.6668 (p0) REVERT: A 546 TYR cc_start: 0.7589 (t80) cc_final: 0.7112 (t80) REVERT: A 890 LYS cc_start: 0.7567 (tttt) cc_final: 0.7319 (tttp) REVERT: B 173 SER cc_start: 0.7411 (m) cc_final: 0.6887 (p) REVERT: C 38 ASP cc_start: 0.6508 (m-30) cc_final: 0.6128 (m-30) outliers start: 17 outliers final: 13 residues processed: 109 average time/residue: 0.1942 time to fit residues: 30.3419 Evaluate side-chains 111 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 96 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 6 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 8642 Z= 0.435 Angle : 0.570 6.162 11831 Z= 0.301 Chirality : 0.044 0.149 1343 Planarity : 0.004 0.048 1425 Dihedral : 11.670 73.934 1417 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.63 % Allowed : 13.47 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.08 (0.26), residues: 979 helix: 0.54 (0.24), residues: 465 sheet: -0.40 (0.50), residues: 98 loop : -0.24 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 916 HIS 0.008 0.002 HIS C 36 PHE 0.020 0.002 PHE A 741 TYR 0.015 0.002 TYR A 453 ARG 0.003 0.000 ARG A 569 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 101 time to evaluate : 1.938 Fit side-chains REVERT: A 144 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6506 (mt-10) REVERT: A 155 ASP cc_start: 0.7888 (m-30) cc_final: 0.7622 (m-30) REVERT: A 160 LYS cc_start: 0.6563 (mmtm) cc_final: 0.6019 (ttmt) REVERT: A 280 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6858 (mp) REVERT: A 890 LYS cc_start: 0.7539 (tttt) cc_final: 0.7175 (tttp) REVERT: A 922 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7152 (tt0) REVERT: B 173 SER cc_start: 0.7490 (m) cc_final: 0.6979 (p) REVERT: C 38 ASP cc_start: 0.6475 (m-30) cc_final: 0.6076 (m-30) outliers start: 23 outliers final: 15 residues processed: 118 average time/residue: 0.2374 time to fit residues: 39.3821 Evaluate side-chains 117 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 922 GLU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 33 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8642 Z= 0.236 Angle : 0.474 5.990 11831 Z= 0.249 Chirality : 0.040 0.144 1343 Planarity : 0.003 0.049 1425 Dihedral : 11.638 74.217 1417 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.05 % Allowed : 14.73 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.32 (0.26), residues: 979 helix: 0.71 (0.24), residues: 465 sheet: -0.03 (0.55), residues: 85 loop : -0.15 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.006 0.001 HIS A 309 PHE 0.016 0.001 PHE A 741 TYR 0.013 0.001 TYR A 453 ARG 0.002 0.000 ARG A 533 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 0.902 Fit side-chains REVERT: A 144 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6434 (mt-10) REVERT: A 155 ASP cc_start: 0.7818 (m-30) cc_final: 0.7583 (m-30) REVERT: A 160 LYS cc_start: 0.6457 (mmtm) cc_final: 0.5926 (ttmt) REVERT: A 280 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6743 (mp) REVERT: A 377 ASP cc_start: 0.8510 (t0) cc_final: 0.6852 (p0) REVERT: A 890 LYS cc_start: 0.7562 (tttt) cc_final: 0.7218 (tttp) REVERT: B 173 SER cc_start: 0.7417 (m) cc_final: 0.6878 (p) REVERT: C 38 ASP cc_start: 0.6513 (m-30) cc_final: 0.6106 (m-30) outliers start: 18 outliers final: 15 residues processed: 114 average time/residue: 0.1990 time to fit residues: 32.0567 Evaluate side-chains 116 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 22 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8642 Z= 0.271 Angle : 0.488 6.037 11831 Z= 0.257 Chirality : 0.040 0.147 1343 Planarity : 0.003 0.051 1425 Dihedral : 11.648 76.531 1417 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.17 % Allowed : 15.53 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.32 (0.26), residues: 979 helix: 0.73 (0.24), residues: 465 sheet: -0.03 (0.55), residues: 85 loop : -0.18 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 916 HIS 0.006 0.001 HIS A 309 PHE 0.017 0.002 PHE A 741 TYR 0.013 0.001 TYR A 453 ARG 0.002 0.000 ARG A 533 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 1.058 Fit side-chains REVERT: A 144 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6436 (mt-10) REVERT: A 155 ASP cc_start: 0.7834 (m-30) cc_final: 0.7579 (m-30) REVERT: A 160 LYS cc_start: 0.6481 (mmtm) cc_final: 0.5928 (ttmt) REVERT: A 280 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6765 (mp) REVERT: A 377 ASP cc_start: 0.8510 (t0) cc_final: 0.6882 (p0) REVERT: A 890 LYS cc_start: 0.7587 (tttt) cc_final: 0.7251 (tttp) REVERT: C 38 ASP cc_start: 0.6499 (m-30) cc_final: 0.6094 (m-30) outliers start: 19 outliers final: 16 residues processed: 112 average time/residue: 0.1999 time to fit residues: 32.2405 Evaluate side-chains 116 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 33 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 0.0170 overall best weight: 2.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8642 Z= 0.271 Angle : 0.486 5.983 11831 Z= 0.257 Chirality : 0.040 0.146 1343 Planarity : 0.003 0.051 1425 Dihedral : 11.669 78.471 1417 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.51 % Allowed : 15.18 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.35 (0.26), residues: 979 helix: 0.78 (0.24), residues: 459 sheet: -0.03 (0.55), residues: 85 loop : -0.19 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 916 HIS 0.006 0.001 HIS A 309 PHE 0.017 0.002 PHE A 741 TYR 0.014 0.001 TYR A 453 ARG 0.002 0.000 ARG A 569 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 0.843 Fit side-chains REVERT: A 138 ASN cc_start: 0.7428 (t0) cc_final: 0.7149 (t0) REVERT: A 144 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6439 (mt-10) REVERT: A 155 ASP cc_start: 0.7821 (m-30) cc_final: 0.7571 (m-30) REVERT: A 160 LYS cc_start: 0.6477 (mmtm) cc_final: 0.5926 (ttmt) REVERT: A 280 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6744 (mp) REVERT: A 377 ASP cc_start: 0.8473 (t0) cc_final: 0.6826 (p0) REVERT: A 890 LYS cc_start: 0.7571 (tttt) cc_final: 0.7244 (tttp) REVERT: C 38 ASP cc_start: 0.6498 (m-30) cc_final: 0.6095 (m-30) outliers start: 22 outliers final: 16 residues processed: 115 average time/residue: 0.1904 time to fit residues: 31.5482 Evaluate side-chains 116 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 33 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.0670 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 94 optimal weight: 8.9990 chunk 57 optimal weight: 0.5980 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8642 Z= 0.171 Angle : 0.442 6.170 11831 Z= 0.232 Chirality : 0.038 0.139 1343 Planarity : 0.003 0.053 1425 Dihedral : 11.643 81.691 1417 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.05 % Allowed : 15.75 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.26), residues: 979 helix: 0.94 (0.25), residues: 458 sheet: 0.02 (0.56), residues: 85 loop : -0.07 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.006 0.001 HIS A 309 PHE 0.015 0.001 PHE A 741 TYR 0.012 0.001 TYR A 453 ARG 0.002 0.000 ARG A 533 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 0.904 Fit side-chains REVERT: A 138 ASN cc_start: 0.7477 (t0) cc_final: 0.7193 (t0) REVERT: A 144 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6333 (mt-10) REVERT: A 155 ASP cc_start: 0.7787 (m-30) cc_final: 0.7552 (m-30) REVERT: A 160 LYS cc_start: 0.6442 (mmtm) cc_final: 0.5668 (pttm) REVERT: A 280 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6685 (mp) REVERT: A 377 ASP cc_start: 0.8291 (t0) cc_final: 0.6732 (p0) REVERT: A 546 TYR cc_start: 0.7497 (t80) cc_final: 0.7018 (t80) REVERT: A 890 LYS cc_start: 0.7521 (tttt) cc_final: 0.7233 (tttp) REVERT: C 38 ASP cc_start: 0.6565 (m-30) cc_final: 0.6177 (m-30) outliers start: 18 outliers final: 15 residues processed: 112 average time/residue: 0.1960 time to fit residues: 31.7110 Evaluate side-chains 113 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 33 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 63 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8642 Z= 0.146 Angle : 0.426 5.999 11831 Z= 0.223 Chirality : 0.037 0.133 1343 Planarity : 0.003 0.052 1425 Dihedral : 11.607 83.710 1417 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.60 % Allowed : 16.10 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.57 (0.26), residues: 979 helix: 0.93 (0.24), residues: 476 sheet: 0.01 (0.56), residues: 85 loop : -0.05 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 PHE 0.014 0.001 PHE A 741 TYR 0.012 0.001 TYR A 453 ARG 0.002 0.000 ARG A 533 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 0.980 Fit side-chains REVERT: A 138 ASN cc_start: 0.7556 (t0) cc_final: 0.7287 (t0) REVERT: A 144 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6335 (mt-10) REVERT: A 155 ASP cc_start: 0.7757 (m-30) cc_final: 0.7539 (m-30) REVERT: A 160 LYS cc_start: 0.6444 (mmtm) cc_final: 0.5689 (pttm) REVERT: A 280 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6650 (mp) REVERT: A 377 ASP cc_start: 0.8166 (t0) cc_final: 0.6629 (p0) REVERT: A 546 TYR cc_start: 0.7475 (t80) cc_final: 0.6993 (t80) REVERT: A 890 LYS cc_start: 0.7497 (tttt) cc_final: 0.7160 (tttp) REVERT: C 38 ASP cc_start: 0.6582 (m-30) cc_final: 0.6203 (m-30) outliers start: 14 outliers final: 12 residues processed: 107 average time/residue: 0.1931 time to fit residues: 29.6253 Evaluate side-chains 111 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 22 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 79 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.0470 chunk 69 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 0.0770 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.157959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.134684 restraints weight = 9038.417| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.19 r_work: 0.3339 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8642 Z= 0.113 Angle : 0.413 5.852 11831 Z= 0.214 Chirality : 0.037 0.128 1343 Planarity : 0.003 0.052 1425 Dihedral : 11.562 85.473 1417 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.37 % Allowed : 16.32 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.83 (0.27), residues: 979 helix: 1.16 (0.24), residues: 476 sheet: 0.02 (0.55), residues: 85 loop : 0.09 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 PHE 0.013 0.001 PHE A 741 TYR 0.012 0.001 TYR A 453 ARG 0.002 0.000 ARG A 533 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1885.79 seconds wall clock time: 35 minutes 10.91 seconds (2110.91 seconds total)