Starting phenix.real_space_refine on Thu Mar 14 18:02:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6r_29779/03_2024/8g6r_29779.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6r_29779/03_2024/8g6r_29779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6r_29779/03_2024/8g6r_29779.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6r_29779/03_2024/8g6r_29779.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6r_29779/03_2024/8g6r_29779.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6r_29779/03_2024/8g6r_29779.pdb" } resolution = 3.4 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= 0.001 sd= 0.016 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 40 5.49 5 S 71 5.16 5 C 5846 2.51 5 N 1565 2.21 5 O 1882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 783": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 852": "OE1" <-> "OE2" Residue "A PHE 910": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "C TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 44": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9406 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7198 Classifications: {'peptide': 899} Link IDs: {'PTRANS': 25, 'TRANS': 873} Chain breaks: 2 Chain: "B" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 878 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "C" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 477 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "I" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 428 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 12, 'rna3p_pyr': 7} Link IDs: {'rna3p': 19} Chain: "J" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 423 Classifications: {'RNA': 20} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 11} Link IDs: {'rna3p': 19} 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 2370 SG CYS A 296 27.578 61.099 83.170 1.00104.05 S ATOM 2408 SG CYS A 301 28.842 64.368 84.713 1.00 97.50 S ATOM 2439 SG CYS A 305 30.494 60.986 85.568 1.00 91.72 S ATOM 3802 SG CYS A 482 18.288 63.589 63.785 1.00111.18 S ATOM 5042 SG CYS A 640 18.703 66.880 65.627 1.00110.13 S ATOM 5048 SG CYS A 641 17.625 63.682 67.468 1.00111.44 S Time building chain proxies: 5.51, per 1000 atoms: 0.59 Number of scatterers: 9406 At special positions: 0 Unit cell: (91.74, 97.578, 124.266, 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 71 16.00 P 40 15.00 O 1882 8.00 N 1565 7.00 C 5846 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: 4.30 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 290 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 305 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 296 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 637 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 641 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 482 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 640 " Number of angles added : 6 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2030 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 11 sheets defined 54.7% alpha, 11.5% beta 14 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 3.10 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 removed outlier: 3.889A pdb=" N ARG A 9 " --> pdb=" O ALA A 5 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL A 10 " --> pdb=" O TYR A 6 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 73 through 86 removed outlier: 4.509A pdb=" N LYS A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 126 Processing helix chain 'A' and resid 133 through 143 Processing helix chain 'A' and resid 147 through 153 removed outlier: 3.812A pdb=" N ASN A 153 " --> pdb=" O TYR A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 194 removed outlier: 4.097A pdb=" N ARG A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A 172 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 228 through 242 removed outlier: 3.760A pdb=" N MET A 235 " --> pdb=" O TYR A 231 " (cutoff:3.500A) Proline residue: A 237 - end of helix Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 262 through 267 Processing helix chain 'A' and resid 270 through 282 Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 298 through 314 removed outlier: 4.074A pdb=" N THR A 314 " --> pdb=" O THR A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 372 removed outlier: 4.707A pdb=" N GLN A 368 " --> pdb=" O ASN A 364 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N CYS A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 379 removed outlier: 4.342A pdb=" N LEU A 376 " --> pdb=" O ASP A 372 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 379 " --> pdb=" O LEU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 422 Processing helix chain 'A' and resid 442 through 449 removed outlier: 3.721A pdb=" N LYS A 446 " --> pdb=" O ASP A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 454 Processing helix chain 'A' and resid 460 through 474 removed outlier: 4.170A pdb=" N VAL A 466 " --> pdb=" O CYS A 462 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A 467 " --> pdb=" O GLN A 463 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR A 474 " --> pdb=" O ILE A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 488 Processing helix chain 'A' and resid 498 through 503 removed outlier: 4.529A pdb=" N LYS A 503 " --> pdb=" O TYR A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 514 removed outlier: 3.996A pdb=" N TYR A 510 " --> pdb=" O LYS A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 527 Processing helix chain 'A' and resid 556 through 577 removed outlier: 3.684A pdb=" N THR A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LYS A 569 " --> pdb=" O GLN A 565 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N HIS A 570 " --> pdb=" O TYR A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 616 through 621 Processing helix chain 'A' and resid 624 through 635 Processing helix chain 'A' and resid 642 through 658 Processing helix chain 'A' and resid 681 through 704 removed outlier: 3.621A pdb=" N ASN A 698 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER A 704 " --> pdb=" O ASN A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 710 removed outlier: 5.805A pdb=" N ASN A 708 " --> pdb=" O VAL A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 727 Processing helix chain 'A' and resid 733 through 747 Processing helix chain 'A' and resid 763 through 768 Processing helix chain 'A' and resid 773 through 784 Processing helix chain 'A' and resid 799 through 803 Processing helix chain 'A' and resid 828 through 837 Processing helix chain 'A' and resid 847 through 862 Processing helix chain 'A' and resid 863 through 867 Processing helix chain 'A' and resid 869 through 890 removed outlier: 3.578A pdb=" N VAL A 875 " --> pdb=" O GLU A 871 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE A 876 " --> pdb=" O TYR A 872 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR A 877 " --> pdb=" O LYS A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 912 Processing helix chain 'A' and resid 912 through 920 removed outlier: 4.280A pdb=" N TYR A 916 " --> pdb=" O ASP A 912 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET A 919 " --> pdb=" O PHE A 915 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR A 920 " --> pdb=" O TYR A 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 97 Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.610A pdb=" N VAL B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 112 removed outlier: 5.825A pdb=" N ASP B 112 " --> pdb=" O LEU B 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 109 through 112' Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 168 through 174 removed outlier: 3.697A pdb=" N VAL B 172 " --> pdb=" O HIS B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'C' and resid 3 through 20 removed outlier: 4.052A pdb=" N VAL C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL C 12 " --> pdb=" O CYS C 8 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET C 20 " --> pdb=" O CYS C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 24 Processing helix chain 'C' and resid 25 through 42 removed outlier: 3.553A pdb=" N TRP C 29 " --> pdb=" O ASN C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 63 removed outlier: 3.597A pdb=" N ALA C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS C 62 " --> pdb=" O PHE C 58 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20 removed outlier: 4.838A pdb=" N PHE A 63 " --> pdb=" O ASP A 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 32 removed outlier: 4.647A pdb=" N VAL A 29 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS A 48 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA4, first strand: chain 'A' and resid 197 through 198 removed outlier: 6.757A pdb=" N GLY A 197 " --> pdb=" O ILE A 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 350 removed outlier: 6.762A pdb=" N LEU A 324 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N TYR A 341 " --> pdb=" O GLY A 322 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLY A 322 " --> pdb=" O TYR A 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 382 through 385 removed outlier: 6.205A pdb=" N ALA A 382 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N VAL B 131 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL A 384 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE B 156 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 392 through 395 removed outlier: 6.200A pdb=" N SER A 392 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU A 670 " --> pdb=" O SER A 392 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA A 394 " --> pdb=" O PHE A 668 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 409 through 410 Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AB1, first strand: chain 'A' and resid 748 through 753 removed outlier: 3.628A pdb=" N SER A 749 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TRP A 795 " --> pdb=" O GLY A 611 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 811 through 817 removed outlier: 3.674A pdb=" N HIS A 811 " --> pdb=" O TYR A 826 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR A 826 " --> pdb=" O HIS A 811 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 3.39 Time building geometry restraints manager: 4.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2799 1.33 - 1.45: 1852 1.45 - 1.57: 4865 1.57 - 1.69: 78 1.69 - 1.81: 100 Bond restraints: 9694 Sorted by residual: bond pdb=" N ASP A 3 " pdb=" CA ASP A 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N LYS C 2 " pdb=" CA LYS C 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.81e+00 bond pdb=" N ARG B 79 " pdb=" CA ARG B 79 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.78e+00 bond pdb=" CB CYS A 651 " pdb=" SG CYS A 651 " ideal model delta sigma weight residual 1.808 1.771 0.037 3.30e-02 9.18e+02 1.28e+00 bond pdb=" CB ASN A 698 " pdb=" CG ASN A 698 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.22e+00 ... (remaining 9689 not shown) Histogram of bond angle deviations from ideal: 97.72 - 104.99: 283 104.99 - 112.26: 4953 112.26 - 119.53: 3233 119.53 - 126.80: 4642 126.80 - 134.07: 208 Bond angle restraints: 13319 Sorted by residual: angle pdb=" C TYR A 782 " pdb=" N TYR A 783 " pdb=" CA TYR A 783 " ideal model delta sigma weight residual 122.38 117.34 5.04 1.81e+00 3.05e-01 7.75e+00 angle pdb=" C GLU C 50 " pdb=" N MET C 51 " pdb=" CA MET C 51 " ideal model delta sigma weight residual 120.28 117.75 2.53 1.34e+00 5.57e-01 3.57e+00 angle pdb=" N TYR A 783 " pdb=" CA TYR A 783 " pdb=" CB TYR A 783 " ideal model delta sigma weight residual 110.44 113.18 -2.74 1.53e+00 4.27e-01 3.20e+00 angle pdb=" N MET C 51 " pdb=" CA MET C 51 " pdb=" CB MET C 51 " ideal model delta sigma weight residual 110.12 112.66 -2.54 1.47e+00 4.63e-01 2.98e+00 angle pdb=" N PRO C 45 " pdb=" CA PRO C 45 " pdb=" C PRO C 45 " ideal model delta sigma weight residual 112.47 115.99 -3.52 2.06e+00 2.36e-01 2.92e+00 ... (remaining 13314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 5248 17.57 - 35.14: 371 35.14 - 52.71: 91 52.71 - 70.28: 49 70.28 - 87.85: 15 Dihedral angle restraints: 5774 sinusoidal: 2611 harmonic: 3163 Sorted by residual: dihedral pdb=" CA GLN A 656 " pdb=" C GLN A 656 " pdb=" N VAL A 657 " pdb=" CA VAL A 657 " ideal model delta harmonic sigma weight residual 180.00 -161.38 -18.62 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA LEU A 125 " pdb=" C LEU A 125 " pdb=" N ARG A 126 " pdb=" CA ARG A 126 " ideal model delta harmonic sigma weight residual 180.00 161.78 18.22 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" O4' G J 25 " pdb=" C1' G J 25 " pdb=" N9 G J 25 " pdb=" C4 G J 25 " ideal model delta sinusoidal sigma weight residual 70.00 6.87 63.13 1 2.00e+01 2.50e-03 1.32e+01 ... (remaining 5771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 931 0.028 - 0.056: 421 0.056 - 0.084: 89 0.084 - 0.112: 66 0.112 - 0.140: 9 Chirality restraints: 1516 Sorted by residual: chirality pdb=" CA PRO C 45 " pdb=" N PRO C 45 " pdb=" C PRO C 45 " pdb=" CB PRO C 45 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CA ILE B 159 " pdb=" N ILE B 159 " pdb=" C ILE B 159 " pdb=" CB ILE B 159 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CA PRO A 863 " pdb=" N PRO A 863 " pdb=" C PRO A 863 " pdb=" CB PRO A 863 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 1513 not shown) Planarity restraints: 1545 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 531 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO A 532 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 532 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 532 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 380 " -0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO A 381 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 381 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 381 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 158 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO A 159 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 159 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 159 " 0.020 5.00e-02 4.00e+02 ... (remaining 1542 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 102 2.51 - 3.11: 8157 3.11 - 3.71: 14949 3.71 - 4.30: 21408 4.30 - 4.90: 33968 Nonbonded interactions: 78584 Sorted by model distance: nonbonded pdb=" OG SER A 809 " pdb=" OP1 A I 33 " model vdw 1.919 2.440 nonbonded pdb=" OG1 THR A 533 " pdb=" OE1 GLN A 656 " model vdw 1.967 2.440 nonbonded pdb=" OD1 ASP A 618 " pdb=" OG1 THR A 675 " model vdw 1.981 2.440 nonbonded pdb=" O LEU A 509 " pdb=" OG SER A 513 " model vdw 1.984 2.440 nonbonded pdb=" OH TYR A 289 " pdb=" OD1 ASN A 309 " model vdw 2.052 2.440 ... (remaining 78579 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: 0.010 Normalize map: mean=0, sd=1: 0.710 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: 4.000 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 32.430 Find NCS groups from input model: 0.220 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 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 : 0.005 0.037 9694 Z= 0.308 Angle : 0.512 6.136 13319 Z= 0.290 Chirality : 0.036 0.140 1516 Planarity : 0.003 0.041 1545 Dihedral : 14.608 87.846 3744 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.26), residues: 1065 helix: 0.50 (0.24), residues: 478 sheet: -1.14 (0.46), residues: 116 loop : -0.45 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 911 HIS 0.010 0.001 HIS A 342 PHE 0.013 0.001 PHE A 648 TYR 0.016 0.002 TYR A 234 ARG 0.008 0.000 ARG A 548 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLU cc_start: 0.7563 (mp0) cc_final: 0.7355 (mp0) REVERT: A 547 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7725 (mp0) REVERT: A 660 GLU cc_start: 0.7104 (pm20) cc_final: 0.6883 (pm20) REVERT: A 698 ASN cc_start: 0.8392 (m110) cc_final: 0.8160 (m110) REVERT: B 137 SER cc_start: 0.9516 (m) cc_final: 0.8964 (p) REVERT: B 159 ILE cc_start: 0.9303 (mp) cc_final: 0.9056 (mt) REVERT: B 160 LYS cc_start: 0.8629 (mmmt) cc_final: 0.8334 (mmmt) REVERT: C 8 CYS cc_start: 0.8537 (p) cc_final: 0.8191 (p) REVERT: C 37 ASN cc_start: 0.9373 (m-40) cc_final: 0.8932 (m-40) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1997 time to fit residues: 49.8035 Evaluate side-chains 147 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.0270 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN A 403 GLN A 421 GLN A 698 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9694 Z= 0.166 Angle : 0.570 10.727 13319 Z= 0.296 Chirality : 0.040 0.162 1516 Planarity : 0.004 0.033 1545 Dihedral : 12.598 78.054 1759 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.22 % Allowed : 8.76 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.27), residues: 1065 helix: 1.01 (0.24), residues: 505 sheet: -0.82 (0.50), residues: 110 loop : 0.10 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 182 HIS 0.003 0.001 HIS A 342 PHE 0.009 0.001 PHE C 58 TYR 0.022 0.001 TYR A 783 ARG 0.003 0.000 ARG A 853 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 177 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.9031 (tpt) cc_final: 0.8603 (tpp) REVERT: A 248 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8407 (mp0) REVERT: A 267 GLU cc_start: 0.7603 (mp0) cc_final: 0.7377 (mp0) REVERT: A 419 LEU cc_start: 0.9145 (mm) cc_final: 0.8744 (mm) REVERT: A 450 TYR cc_start: 0.8679 (m-80) cc_final: 0.8433 (m-80) REVERT: A 534 MET cc_start: 0.8661 (mpp) cc_final: 0.8353 (mpp) REVERT: A 660 GLU cc_start: 0.7356 (pm20) cc_final: 0.7137 (pm20) REVERT: A 887 TYR cc_start: 0.8651 (t80) cc_final: 0.8154 (t80) REVERT: A 919 MET cc_start: 0.8911 (mmt) cc_final: 0.8622 (mmt) REVERT: B 137 SER cc_start: 0.9637 (m) cc_final: 0.9273 (p) REVERT: B 159 ILE cc_start: 0.9315 (mp) cc_final: 0.8913 (mp) REVERT: B 160 LYS cc_start: 0.8893 (mmmt) cc_final: 0.8667 (mmmt) REVERT: B 165 LYS cc_start: 0.9299 (ptmm) cc_final: 0.8971 (ptmm) REVERT: C 8 CYS cc_start: 0.8495 (p) cc_final: 0.8097 (p) REVERT: C 35 LEU cc_start: 0.9085 (tp) cc_final: 0.8838 (tp) REVERT: C 38 LYS cc_start: 0.8735 (ptmm) cc_final: 0.8337 (ptmm) REVERT: C 46 GLU cc_start: 0.8932 (pm20) cc_final: 0.8731 (pm20) outliers start: 21 outliers final: 12 residues processed: 183 average time/residue: 0.1906 time to fit residues: 49.8518 Evaluate side-chains 165 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 153 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 99 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN A 364 ASN A 403 GLN ** A 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9694 Z= 0.186 Angle : 0.556 13.415 13319 Z= 0.280 Chirality : 0.039 0.186 1516 Planarity : 0.003 0.039 1545 Dihedral : 12.500 78.676 1759 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.95 % Allowed : 11.60 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.27), residues: 1065 helix: 1.17 (0.24), residues: 501 sheet: -0.69 (0.52), residues: 108 loop : 0.17 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 98 HIS 0.004 0.001 HIS B 148 PHE 0.016 0.001 PHE C 58 TYR 0.022 0.002 TYR A 211 ARG 0.006 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 166 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.9069 (tpt) cc_final: 0.8664 (tpp) REVERT: A 267 GLU cc_start: 0.7602 (mp0) cc_final: 0.7327 (mp0) REVERT: A 419 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8850 (mm) REVERT: A 450 TYR cc_start: 0.8677 (m-80) cc_final: 0.8443 (m-80) REVERT: A 534 MET cc_start: 0.8685 (mpp) cc_final: 0.8301 (mpp) REVERT: A 614 TYR cc_start: 0.8604 (m-10) cc_final: 0.8390 (m-10) REVERT: A 660 GLU cc_start: 0.7403 (pm20) cc_final: 0.7114 (pm20) REVERT: A 887 TYR cc_start: 0.8740 (t80) cc_final: 0.7702 (t80) REVERT: A 919 MET cc_start: 0.8910 (mmt) cc_final: 0.8623 (mmt) REVERT: B 91 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7356 (tt) REVERT: B 137 SER cc_start: 0.9677 (m) cc_final: 0.9284 (p) REVERT: B 159 ILE cc_start: 0.9320 (mp) cc_final: 0.8930 (mp) REVERT: B 160 LYS cc_start: 0.8982 (mmmt) cc_final: 0.8728 (mmmt) REVERT: B 165 LYS cc_start: 0.9321 (ptmm) cc_final: 0.9087 (ptmm) REVERT: C 8 CYS cc_start: 0.8553 (p) cc_final: 0.8349 (p) REVERT: C 20 MET cc_start: 0.8155 (ptp) cc_final: 0.7954 (ptt) REVERT: C 38 LYS cc_start: 0.8762 (ptmm) cc_final: 0.8422 (ptmm) REVERT: C 46 GLU cc_start: 0.8998 (pm20) cc_final: 0.8752 (pm20) outliers start: 28 outliers final: 15 residues processed: 180 average time/residue: 0.1989 time to fit residues: 51.1636 Evaluate side-chains 172 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 155 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 26 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 7.9990 chunk 75 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 100 optimal weight: 0.0270 chunk 106 optimal weight: 40.0000 chunk 52 optimal weight: 0.5980 chunk 95 optimal weight: 8.9990 chunk 28 optimal weight: 0.3980 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN ** A 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9694 Z= 0.149 Angle : 0.560 13.541 13319 Z= 0.277 Chirality : 0.039 0.250 1516 Planarity : 0.003 0.043 1545 Dihedral : 12.435 78.347 1759 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.53 % Allowed : 14.66 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.27), residues: 1065 helix: 1.28 (0.24), residues: 492 sheet: -0.65 (0.53), residues: 108 loop : 0.32 (0.31), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 182 HIS 0.002 0.001 HIS A 304 PHE 0.011 0.001 PHE A 736 TYR 0.022 0.001 TYR A 211 ARG 0.008 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 170 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.9007 (tpt) cc_final: 0.8469 (tpp) REVERT: A 267 GLU cc_start: 0.7644 (mp0) cc_final: 0.7306 (mp0) REVERT: A 403 GLN cc_start: 0.8499 (tt0) cc_final: 0.8044 (pm20) REVERT: A 419 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8903 (mm) REVERT: A 534 MET cc_start: 0.8665 (mpp) cc_final: 0.8248 (mpp) REVERT: A 660 GLU cc_start: 0.7378 (pm20) cc_final: 0.7042 (pm20) REVERT: A 919 MET cc_start: 0.8846 (mmt) cc_final: 0.8562 (mmt) REVERT: B 137 SER cc_start: 0.9555 (m) cc_final: 0.9231 (p) REVERT: B 159 ILE cc_start: 0.9278 (mp) cc_final: 0.8853 (mp) REVERT: B 160 LYS cc_start: 0.9020 (mmmt) cc_final: 0.8730 (mmmt) REVERT: B 171 GLU cc_start: 0.8745 (mp0) cc_final: 0.8334 (pm20) REVERT: C 8 CYS cc_start: 0.8548 (p) cc_final: 0.8317 (p) REVERT: C 35 LEU cc_start: 0.9074 (tp) cc_final: 0.8820 (tp) REVERT: C 38 LYS cc_start: 0.8728 (ptmm) cc_final: 0.8277 (ptmm) REVERT: C 46 GLU cc_start: 0.8990 (pm20) cc_final: 0.8770 (pm20) outliers start: 24 outliers final: 17 residues processed: 181 average time/residue: 0.1998 time to fit residues: 51.5066 Evaluate side-chains 173 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 155 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 777 PHE Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 GLN ** A 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 HIS B 168 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 9694 Z= 0.371 Angle : 0.625 11.589 13319 Z= 0.317 Chirality : 0.041 0.232 1516 Planarity : 0.004 0.033 1545 Dihedral : 12.519 79.821 1759 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.22 % Allowed : 15.30 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.27), residues: 1065 helix: 1.00 (0.24), residues: 506 sheet: -0.62 (0.54), residues: 106 loop : 0.10 (0.32), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 182 HIS 0.005 0.001 HIS A 342 PHE 0.013 0.001 PHE A 692 TYR 0.027 0.002 TYR A 211 ARG 0.005 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 154 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 MET cc_start: 0.8609 (pmm) cc_final: 0.8387 (pmm) REVERT: A 267 GLU cc_start: 0.7745 (mp0) cc_final: 0.7407 (mp0) REVERT: A 403 GLN cc_start: 0.8577 (tt0) cc_final: 0.8177 (pm20) REVERT: A 419 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8942 (mm) REVERT: A 614 TYR cc_start: 0.8666 (m-10) cc_final: 0.8461 (m-10) REVERT: A 919 MET cc_start: 0.8944 (mmt) cc_final: 0.8686 (mmt) REVERT: B 140 ARG cc_start: 0.8599 (mtm-85) cc_final: 0.8322 (mtm-85) REVERT: B 159 ILE cc_start: 0.9244 (mp) cc_final: 0.8590 (mp) REVERT: B 160 LYS cc_start: 0.9089 (mmmt) cc_final: 0.8689 (mmmt) REVERT: C 8 CYS cc_start: 0.8648 (p) cc_final: 0.8410 (p) REVERT: C 35 LEU cc_start: 0.9109 (tp) cc_final: 0.8877 (tp) REVERT: C 38 LYS cc_start: 0.8750 (ptmm) cc_final: 0.8395 (ptmm) REVERT: C 51 MET cc_start: 0.9260 (mpp) cc_final: 0.8941 (mpp) outliers start: 40 outliers final: 26 residues processed: 174 average time/residue: 0.1872 time to fit residues: 46.7555 Evaluate side-chains 177 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 150 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 777 PHE Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain C residue 2 LYS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 26 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.0020 chunk 95 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 30.0000 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 8 optimal weight: 0.2980 chunk 55 optimal weight: 5.9990 chunk 102 optimal weight: 0.0060 overall best weight: 0.6608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 918 ASN B 148 HIS B 168 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9694 Z= 0.145 Angle : 0.553 12.502 13319 Z= 0.275 Chirality : 0.039 0.315 1516 Planarity : 0.003 0.030 1545 Dihedral : 12.471 80.032 1759 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.06 % Allowed : 16.14 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.27), residues: 1065 helix: 1.20 (0.24), residues: 497 sheet: -0.54 (0.58), residues: 94 loop : 0.21 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 182 HIS 0.010 0.001 HIS B 168 PHE 0.010 0.001 PHE A 736 TYR 0.024 0.001 TYR A 663 ARG 0.006 0.000 ARG A 548 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 160 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 TYR cc_start: 0.7593 (p90) cc_final: 0.7364 (p90) REVERT: A 267 GLU cc_start: 0.7691 (mp0) cc_final: 0.7316 (mp0) REVERT: A 403 GLN cc_start: 0.8535 (tt0) cc_final: 0.8077 (pm20) REVERT: A 412 LYS cc_start: 0.9301 (tttp) cc_final: 0.9007 (tppt) REVERT: A 419 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8917 (mm) REVERT: A 534 MET cc_start: 0.8670 (mpp) cc_final: 0.8400 (mpp) REVERT: A 919 MET cc_start: 0.8844 (mmt) cc_final: 0.8595 (mmt) REVERT: B 136 ASP cc_start: 0.9349 (m-30) cc_final: 0.9107 (m-30) REVERT: B 137 SER cc_start: 0.9446 (m) cc_final: 0.8786 (p) REVERT: B 159 ILE cc_start: 0.9222 (mp) cc_final: 0.8804 (mp) REVERT: B 160 LYS cc_start: 0.9090 (mmmt) cc_final: 0.8772 (mmmt) REVERT: B 171 GLU cc_start: 0.8936 (mp0) cc_final: 0.8624 (pm20) REVERT: C 8 CYS cc_start: 0.8559 (p) cc_final: 0.8247 (p) REVERT: C 35 LEU cc_start: 0.9101 (tp) cc_final: 0.8872 (tp) REVERT: C 38 LYS cc_start: 0.8719 (ptmm) cc_final: 0.8364 (ptmm) REVERT: C 41 LEU cc_start: 0.8844 (mm) cc_final: 0.8632 (mm) REVERT: C 46 GLU cc_start: 0.8890 (pm20) cc_final: 0.8689 (pm20) outliers start: 29 outliers final: 24 residues processed: 175 average time/residue: 0.1976 time to fit residues: 49.3807 Evaluate side-chains 181 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 156 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 777 PHE Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 918 ASN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain C residue 3 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 5.9990 chunk 60 optimal weight: 0.3980 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 106 optimal weight: 30.0000 chunk 66 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 48 optimal weight: 0.0770 chunk 65 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 overall best weight: 1.2140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 918 ASN B 148 HIS B 168 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9694 Z= 0.177 Angle : 0.566 13.014 13319 Z= 0.280 Chirality : 0.039 0.287 1516 Planarity : 0.003 0.031 1545 Dihedral : 12.386 80.366 1759 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.27 % Allowed : 16.77 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.27), residues: 1065 helix: 1.23 (0.24), residues: 493 sheet: -0.69 (0.59), residues: 88 loop : 0.21 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 182 HIS 0.003 0.001 HIS A 304 PHE 0.011 0.001 PHE A 736 TYR 0.026 0.001 TYR A 887 ARG 0.012 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 159 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 TYR cc_start: 0.7624 (p90) cc_final: 0.7390 (p90) REVERT: A 267 GLU cc_start: 0.7719 (mp0) cc_final: 0.7343 (mp0) REVERT: A 403 GLN cc_start: 0.8543 (tt0) cc_final: 0.8117 (pm20) REVERT: A 412 LYS cc_start: 0.9314 (tttp) cc_final: 0.8954 (tppt) REVERT: A 419 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8950 (mm) REVERT: A 534 MET cc_start: 0.8631 (mpp) cc_final: 0.8332 (mpp) REVERT: A 536 GLN cc_start: 0.7671 (tt0) cc_final: 0.7251 (mt0) REVERT: A 887 TYR cc_start: 0.8668 (t80) cc_final: 0.8232 (t80) REVERT: B 137 SER cc_start: 0.9437 (m) cc_final: 0.8910 (p) REVERT: B 159 ILE cc_start: 0.9205 (mp) cc_final: 0.8764 (mp) REVERT: B 160 LYS cc_start: 0.9102 (mmmt) cc_final: 0.8789 (mmmt) REVERT: B 171 GLU cc_start: 0.8941 (mp0) cc_final: 0.8639 (pm20) REVERT: C 8 CYS cc_start: 0.8544 (p) cc_final: 0.8314 (p) REVERT: C 35 LEU cc_start: 0.9129 (tp) cc_final: 0.8866 (tp) REVERT: C 38 LYS cc_start: 0.8664 (ptmm) cc_final: 0.8218 (ptmm) REVERT: C 46 GLU cc_start: 0.8903 (pm20) cc_final: 0.8701 (pm20) REVERT: C 47 LYS cc_start: 0.9547 (mmtt) cc_final: 0.9332 (mmtt) outliers start: 31 outliers final: 22 residues processed: 176 average time/residue: 0.2023 time to fit residues: 50.4689 Evaluate side-chains 176 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 153 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 777 PHE Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 918 ASN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain C residue 3 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 9694 Z= 0.434 Angle : 0.688 13.191 13319 Z= 0.349 Chirality : 0.043 0.262 1516 Planarity : 0.004 0.035 1545 Dihedral : 12.495 82.837 1759 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.11 % Allowed : 16.35 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.27), residues: 1065 helix: 0.72 (0.24), residues: 506 sheet: -0.84 (0.57), residues: 98 loop : -0.07 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP B 182 HIS 0.007 0.002 HIS A 342 PHE 0.017 0.002 PHE A 692 TYR 0.029 0.002 TYR A 211 ARG 0.010 0.001 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 151 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 GLU cc_start: 0.7799 (mp0) cc_final: 0.7346 (mp0) REVERT: A 403 GLN cc_start: 0.8538 (tt0) cc_final: 0.8121 (pm20) REVERT: A 412 LYS cc_start: 0.9341 (tttp) cc_final: 0.9038 (tppt) REVERT: A 419 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8971 (mm) REVERT: A 534 MET cc_start: 0.8777 (mpp) cc_final: 0.8429 (mpp) REVERT: A 614 TYR cc_start: 0.8711 (m-10) cc_final: 0.8488 (m-10) REVERT: B 137 SER cc_start: 0.9444 (m) cc_final: 0.9152 (p) REVERT: B 159 ILE cc_start: 0.9268 (mp) cc_final: 0.8697 (mp) REVERT: B 160 LYS cc_start: 0.9130 (mmmt) cc_final: 0.8724 (mmmt) REVERT: C 8 CYS cc_start: 0.8635 (p) cc_final: 0.8395 (p) REVERT: C 38 LYS cc_start: 0.8687 (ptmm) cc_final: 0.8281 (ptmm) REVERT: C 46 GLU cc_start: 0.8959 (pm20) cc_final: 0.8713 (pm20) outliers start: 39 outliers final: 32 residues processed: 171 average time/residue: 0.1981 time to fit residues: 48.3543 Evaluate side-chains 180 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 147 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 777 PHE Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 26 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9694 Z= 0.166 Angle : 0.593 13.746 13319 Z= 0.294 Chirality : 0.040 0.334 1516 Planarity : 0.003 0.033 1545 Dihedral : 12.419 82.272 1759 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.22 % Allowed : 19.09 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.27), residues: 1065 helix: 1.02 (0.24), residues: 504 sheet: -0.65 (0.56), residues: 100 loop : 0.04 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 182 HIS 0.003 0.001 HIS A 342 PHE 0.010 0.001 PHE A 736 TYR 0.025 0.001 TYR A 211 ARG 0.015 0.001 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 153 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 TYR cc_start: 0.7611 (p90) cc_final: 0.7377 (p90) REVERT: A 267 GLU cc_start: 0.7706 (mp0) cc_final: 0.7315 (mp0) REVERT: A 412 LYS cc_start: 0.9310 (tttp) cc_final: 0.8965 (tppt) REVERT: A 419 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8959 (mm) REVERT: A 534 MET cc_start: 0.8703 (mpp) cc_final: 0.8368 (mpp) REVERT: A 536 GLN cc_start: 0.7760 (tt0) cc_final: 0.7234 (mt0) REVERT: B 134 ASP cc_start: 0.8335 (t0) cc_final: 0.7955 (t70) REVERT: B 137 SER cc_start: 0.9410 (m) cc_final: 0.9164 (p) REVERT: B 159 ILE cc_start: 0.9237 (mp) cc_final: 0.8716 (mp) REVERT: B 160 LYS cc_start: 0.9153 (mmmt) cc_final: 0.8763 (mmmt) REVERT: C 8 CYS cc_start: 0.8565 (p) cc_final: 0.8306 (p) REVERT: C 38 LYS cc_start: 0.8597 (ptmm) cc_final: 0.8340 (ptmm) REVERT: C 46 GLU cc_start: 0.8915 (pm20) cc_final: 0.8671 (pm20) outliers start: 21 outliers final: 16 residues processed: 162 average time/residue: 0.1953 time to fit residues: 45.5379 Evaluate side-chains 167 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 150 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 777 PHE Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 188 CYS Chi-restraints excluded: chain C residue 3 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 109 optimal weight: 20.0000 chunk 100 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 53 optimal weight: 0.0970 chunk 69 optimal weight: 3.9990 chunk 92 optimal weight: 0.0770 chunk 26 optimal weight: 0.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN ** A 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9694 Z= 0.153 Angle : 0.603 13.920 13319 Z= 0.295 Chirality : 0.040 0.343 1516 Planarity : 0.003 0.031 1545 Dihedral : 12.336 81.379 1759 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.22 % Allowed : 18.57 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.27), residues: 1065 helix: 1.14 (0.24), residues: 499 sheet: -0.80 (0.55), residues: 98 loop : 0.05 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 911 HIS 0.003 0.001 HIS A 93 PHE 0.010 0.001 PHE A 736 TYR 0.025 0.001 TYR A 887 ARG 0.013 0.000 ARG B 140 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 155 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 TYR cc_start: 0.7565 (p90) cc_final: 0.7305 (p90) REVERT: A 267 GLU cc_start: 0.7697 (mp0) cc_final: 0.7286 (mp0) REVERT: A 412 LYS cc_start: 0.9310 (tttp) cc_final: 0.8960 (tppt) REVERT: A 534 MET cc_start: 0.8602 (mpp) cc_final: 0.8249 (mpp) REVERT: A 536 GLN cc_start: 0.7770 (tt0) cc_final: 0.7254 (mt0) REVERT: A 919 MET cc_start: 0.8804 (mmt) cc_final: 0.8281 (mmt) REVERT: B 134 ASP cc_start: 0.8179 (t0) cc_final: 0.7622 (t0) REVERT: B 137 SER cc_start: 0.9434 (m) cc_final: 0.9050 (p) REVERT: B 159 ILE cc_start: 0.9233 (mp) cc_final: 0.8874 (mp) REVERT: B 160 LYS cc_start: 0.9163 (mmmt) cc_final: 0.8804 (mmmt) REVERT: C 8 CYS cc_start: 0.8566 (p) cc_final: 0.8307 (p) REVERT: C 38 LYS cc_start: 0.8577 (ptmm) cc_final: 0.8282 (ptmm) outliers start: 21 outliers final: 16 residues processed: 164 average time/residue: 0.1981 time to fit residues: 46.2575 Evaluate side-chains 167 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 151 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 623 ASN Chi-restraints excluded: chain A residue 777 PHE Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 168 HIS Chi-restraints excluded: chain C residue 3 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.0040 chunk 87 optimal weight: 8.9990 chunk 36 optimal weight: 0.1980 chunk 89 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.0770 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 63 optimal weight: 7.9990 overall best weight: 0.3952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.113761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.079209 restraints weight = 22604.933| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.62 r_work: 0.3194 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 9694 Z= 0.151 Angle : 0.594 13.669 13319 Z= 0.291 Chirality : 0.039 0.334 1516 Planarity : 0.004 0.042 1545 Dihedral : 12.311 80.521 1759 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.90 % Allowed : 18.99 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.27), residues: 1065 helix: 1.23 (0.24), residues: 490 sheet: -0.77 (0.57), residues: 93 loop : 0.04 (0.31), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 911 HIS 0.003 0.000 HIS A 93 PHE 0.010 0.001 PHE A 736 TYR 0.031 0.001 TYR A 415 ARG 0.013 0.000 ARG B 140 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2210.51 seconds wall clock time: 40 minutes 30.82 seconds (2430.82 seconds total)