Starting phenix.real_space_refine on Wed Feb 14 09:38:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pu7_13654/02_2024/7pu7_13654_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pu7_13654/02_2024/7pu7_13654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pu7_13654/02_2024/7pu7_13654.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pu7_13654/02_2024/7pu7_13654.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pu7_13654/02_2024/7pu7_13654_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pu7_13654/02_2024/7pu7_13654_updated.pdb" } resolution = 2.9 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 3 6.06 5 P 33 5.49 5 S 37 5.16 5 C 5565 2.51 5 N 1587 2.21 5 O 1765 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 18": "OE1" <-> "OE2" Residue "A GLU 36": "OE1" <-> "OE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A GLU 348": "OE1" <-> "OE2" Residue "A ARG 382": "NH1" <-> "NH2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A ARG 467": "NH1" <-> "NH2" Residue "A TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 480": "NH1" <-> "NH2" Residue "A GLU 505": "OE1" <-> "OE2" Residue "A TYR 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 509": "OE1" <-> "OE2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A GLU 518": "OE1" <-> "OE2" Residue "A GLU 534": "OE1" <-> "OE2" Residue "A TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 605": "NH1" <-> "NH2" Residue "A ARG 608": "NH1" <-> "NH2" Residue "A TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A ARG 719": "NH1" <-> "NH2" Residue "A ARG 731": "NH1" <-> "NH2" Residue "A GLU 752": "OE1" <-> "OE2" Residue "A PHE 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 808": "OE1" <-> "OE2" Residue "A GLU 906": "OE1" <-> "OE2" Residue "A ARG 921": "NH1" <-> "NH2" Residue "A ASP 930": "OD1" <-> "OD2" Residue "A PHE 964": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 971": "OD1" <-> "OD2" Residue "A GLU 974": "OE1" <-> "OE2" Residue "A GLU 982": "OE1" <-> "OE2" Residue "A GLU 1057": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8990 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8267 Classifications: {'peptide': 1070} Link IDs: {'PTRANS': 53, 'TRANS': 1016} Chain breaks: 1 Chain: "T" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 400 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "P" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 280 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 43 Unusual residues: {' ZN': 3, '82W': 1} Classifications: {'undetermined': 4, 'water': 3} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1148 SG CYS A 158 64.073 79.106 65.092 1.00 45.51 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1 82W A1204 " occ=0.00 ... (35 atoms not shown) pdb=" O7 82W A1204 " occ=0.00 Time building chain proxies: 5.34, per 1000 atoms: 0.59 Number of scatterers: 8990 At special positions: 0 Unit cell: (101.322, 108.25, 112.58, 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 3 29.99 S 37 16.00 P 33 15.00 O 1765 8.00 N 1587 7.00 C 5565 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: 3.40 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1201 " pdb="ZN ZN A1201 " - pdb=" SG CYS A 158 " pdb="ZN ZN A1201 " - pdb=" ND1 HIS A 107 " pdb=" ZN A1202 " pdb="ZN ZN A1202 " - pdb=" NE2 HIS A 14 " pdb="ZN ZN A1202 " - pdb=" NE2 HIS A 16 " pdb=" ZN A1203 " pdb="ZN ZN A1203 " - pdb=" NE2 HIS A 228 " pdb="ZN ZN A1203 " - pdb=" NE2 HIS A 48 " 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1954 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 7 sheets defined 48.2% alpha, 8.7% beta 13 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 4.46 Creating SS restraints... Processing helix chain 'A' and resid 28 through 37 Processing helix chain 'A' and resid 54 through 64 Processing helix chain 'A' and resid 100 through 103 No H-bonds generated for 'chain 'A' and resid 100 through 103' Processing helix chain 'A' and resid 115 through 131 removed outlier: 3.546A pdb=" N SER A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 147 removed outlier: 3.633A pdb=" N ALA A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU A 147 " --> pdb=" O GLU A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 147' Processing helix chain 'A' and resid 162 through 169 Processing helix chain 'A' and resid 172 through 186 Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 201 through 217 removed outlier: 4.148A pdb=" N VAL A 206 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASP A 208 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLY A 209 " --> pdb=" O ARG A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 246 removed outlier: 4.309A pdb=" N HIS A 236 " --> pdb=" O ASP A 233 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 242 " --> pdb=" O GLU A 239 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR A 246 " --> pdb=" O CYS A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 removed outlier: 3.560A pdb=" N ILE A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 292 removed outlier: 4.135A pdb=" N THR A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU A 287 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) 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 317 through 332 Processing helix chain 'A' and resid 341 through 354 Processing helix chain 'A' and resid 358 through 374 Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 401 through 404 No H-bonds generated for 'chain 'A' and resid 401 through 404' Processing helix chain 'A' and resid 408 through 411 No H-bonds generated for 'chain 'A' and resid 408 through 411' Processing helix chain 'A' and resid 431 through 442 removed outlier: 3.635A pdb=" N VAL A 435 " --> pdb=" O ARG A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 470 removed outlier: 3.664A pdb=" N LYS A 463 " --> pdb=" O LYS A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.732A pdb=" N PHE A 475 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA A 476 " --> pdb=" O PRO A 473 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS A 483 " --> pdb=" O ARG A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 500 Processing helix chain 'A' and resid 507 through 519 removed outlier: 3.554A pdb=" N ALA A 511 " --> pdb=" O LYS A 508 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLU A 512 " --> pdb=" O GLU A 509 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A 518 " --> pdb=" O GLY A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 532 removed outlier: 3.534A pdb=" N THR A 529 " --> pdb=" O THR A 525 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY A 532 " --> pdb=" O GLN A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 556 No H-bonds generated for 'chain 'A' and resid 554 through 556' Processing helix chain 'A' and resid 575 through 581 removed outlier: 3.991A pdb=" N ILE A 581 " --> pdb=" O ALA A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 607 Processing helix chain 'A' and resid 614 through 616 No H-bonds generated for 'chain 'A' and resid 614 through 616' Processing helix chain 'A' and resid 622 through 630 Processing helix chain 'A' and resid 642 through 651 removed outlier: 3.706A pdb=" N ASP A 646 " --> pdb=" O GLY A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 665 removed outlier: 3.778A pdb=" N ILE A 663 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA A 664 " --> pdb=" O VAL A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 683 removed outlier: 3.521A pdb=" N ALA A 680 " --> pdb=" O HIS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 696 No H-bonds generated for 'chain 'A' and resid 694 through 696' Processing helix chain 'A' and resid 714 through 725 Processing helix chain 'A' and resid 729 through 741 removed outlier: 3.540A pdb=" N ILE A 734 " --> pdb=" O ALA A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 761 removed outlier: 3.626A pdb=" N GLU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 777 removed outlier: 3.547A pdb=" N TRP A 772 " --> pdb=" O ILE A 768 " (cutoff:3.500A) Proline residue: A 777 - end of helix Processing helix chain 'A' and resid 785 through 804 removed outlier: 3.689A pdb=" N VAL A 794 " --> pdb=" O GLY A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 816 removed outlier: 3.628A pdb=" N GLY A 812 " --> pdb=" O GLU A 808 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 816 " --> pdb=" O GLY A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 834 removed outlier: 3.515A pdb=" N ARG A 832 " --> pdb=" O LEU A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 863 No H-bonds generated for 'chain 'A' and resid 861 through 863' Processing helix chain 'A' and resid 869 through 881 Processing helix chain 'A' and resid 888 through 894 Processing helix chain 'A' and resid 897 through 899 No H-bonds generated for 'chain 'A' and resid 897 through 899' Processing helix chain 'A' and resid 902 through 911 Processing helix chain 'A' and resid 921 through 939 removed outlier: 4.470A pdb=" N SER A 929 " --> pdb=" O PHE A 925 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ASP A 930 " --> pdb=" O LEU A 926 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 986 Processing helix chain 'A' and resid 999 through 1005 removed outlier: 3.884A pdb=" N GLN A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1015 Processing helix chain 'A' and resid 1062 through 1067 removed outlier: 3.501A pdb=" N SER A1067 " --> pdb=" O HIS A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1071 No H-bonds generated for 'chain 'A' and resid 1069 through 1071' Processing sheet with id= A, first strand: chain 'A' and resid 42 through 48 removed outlier: 6.330A pdb=" N LYS A 67 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N MET A 45 " --> pdb=" O LYS A 67 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE A 69 " --> pdb=" O MET A 45 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N ASP A 47 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N GLY A 71 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE A 70 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N THR A 109 " --> pdb=" O THR A 155 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 193 through 195 Processing sheet with id= C, first strand: chain 'A' and resid 423 through 427 removed outlier: 9.455A pdb=" N ILE A 424 " --> pdb=" O LYS A 585 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASP A 587 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N PHE A 426 " --> pdb=" O ASP A 587 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N LEU A 589 " --> pdb=" O PHE A 426 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 451 through 453 Processing sheet with id= E, first strand: chain 'A' and resid 560 through 562 Processing sheet with id= F, first strand: chain 'A' and resid 837 through 839 removed outlier: 3.542A pdb=" N ALA A 851 " --> pdb=" O ARG A 858 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1023 through 1029 removed outlier: 3.742A pdb=" N ASP A1097 " --> pdb=" O ASN A1081 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LYS A1083 " --> pdb=" O ALA A1095 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ALA A1095 " --> pdb=" O LYS A1083 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA A1085 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LEU A1093 " --> pdb=" O ALA A1085 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ARG A1087 " --> pdb=" O ILE A1091 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ILE A1091 " --> pdb=" O ARG A1087 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLU A1057 " --> pdb=" O ILE A1091 " (cutoff:3.500A) 319 hydrogen bonds defined for protein. 876 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 3.27 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1903 1.33 - 1.46: 2682 1.46 - 1.58: 4532 1.58 - 1.70: 64 1.70 - 1.82: 65 Bond restraints: 9246 Sorted by residual: bond pdb=" C4 82W A1204 " pdb=" C5 82W A1204 " ideal model delta sigma weight residual 1.510 1.356 0.154 2.00e-02 2.50e+03 5.93e+01 bond pdb=" C1 82W A1204 " pdb=" C2 82W A1204 " ideal model delta sigma weight residual 1.532 1.381 0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" C1' 82W A1204 " pdb=" C2' 82W A1204 " ideal model delta sigma weight residual 1.451 1.314 0.137 2.00e-02 2.50e+03 4.72e+01 bond pdb=" C13 82W A1204 " pdb=" C14 82W A1204 " ideal model delta sigma weight residual 1.510 1.374 0.136 2.00e-02 2.50e+03 4.63e+01 bond pdb=" C6 82W A1204 " pdb=" C7 82W A1204 " ideal model delta sigma weight residual 1.500 1.367 0.133 2.00e-02 2.50e+03 4.40e+01 ... (remaining 9241 not shown) Histogram of bond angle deviations from ideal: 97.88 - 105.21: 357 105.21 - 112.54: 4244 112.54 - 119.87: 4019 119.87 - 127.20: 3918 127.20 - 134.53: 143 Bond angle restraints: 12681 Sorted by residual: angle pdb=" N LYS A 743 " pdb=" CA LYS A 743 " pdb=" C LYS A 743 " ideal model delta sigma weight residual 109.59 98.76 10.83 1.47e+00 4.63e-01 5.43e+01 angle pdb=" N PRO A 670 " pdb=" CA PRO A 670 " pdb=" C PRO A 670 " ideal model delta sigma weight residual 112.47 123.66 -11.19 2.06e+00 2.36e-01 2.95e+01 angle pdb=" C ALA A1009 " pdb=" N ILE A1010 " pdb=" CA ILE A1010 " ideal model delta sigma weight residual 120.24 123.52 -3.28 6.30e-01 2.52e+00 2.71e+01 angle pdb=" N ALA A1045 " pdb=" CA ALA A1045 " pdb=" C ALA A1045 " ideal model delta sigma weight residual 109.23 117.21 -7.98 1.55e+00 4.16e-01 2.65e+01 angle pdb=" C MET A 671 " pdb=" N GLY A 672 " pdb=" CA GLY A 672 " ideal model delta sigma weight residual 120.00 125.21 -5.21 1.10e+00 8.26e-01 2.24e+01 ... (remaining 12676 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.65: 4999 22.65 - 45.29: 417 45.29 - 67.93: 102 67.93 - 90.58: 8 90.58 - 113.22: 1 Dihedral angle restraints: 5527 sinusoidal: 2468 harmonic: 3059 Sorted by residual: dihedral pdb=" CA SER A 20 " pdb=" C SER A 20 " pdb=" N MET A 21 " pdb=" CA MET A 21 " ideal model delta harmonic sigma weight residual -180.00 -156.42 -23.58 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" C PHE A1061 " pdb=" N PHE A1061 " pdb=" CA PHE A1061 " pdb=" CB PHE A1061 " ideal model delta harmonic sigma weight residual -122.60 -133.48 10.88 0 2.50e+00 1.60e-01 1.90e+01 dihedral pdb=" C THR A 774 " pdb=" N THR A 774 " pdb=" CA THR A 774 " pdb=" CB THR A 774 " ideal model delta harmonic sigma weight residual -122.00 -132.04 10.04 0 2.50e+00 1.60e-01 1.61e+01 ... (remaining 5524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 900 0.092 - 0.184: 389 0.184 - 0.276: 89 0.276 - 0.367: 21 0.367 - 0.459: 3 Chirality restraints: 1402 Sorted by residual: chirality pdb=" CA PRO A 670 " pdb=" N PRO A 670 " pdb=" C PRO A 670 " pdb=" CB PRO A 670 " both_signs ideal model delta sigma weight residual False 2.72 2.26 0.46 2.00e-01 2.50e+01 5.27e+00 chirality pdb=" C7 82W A1204 " pdb=" C12 82W A1204 " pdb=" C6 82W A1204 " pdb=" C8 82W A1204 " both_signs ideal model delta sigma weight residual False -2.93 -2.51 -0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" CA PHE A1061 " pdb=" N PHE A1061 " pdb=" C PHE A1061 " pdb=" CB PHE A1061 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 ... (remaining 1399 not shown) Planarity restraints: 1543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 490 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.40e+00 pdb=" C MET A 490 " 0.036 2.00e-02 2.50e+03 pdb=" O MET A 490 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA A 491 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 197 " 0.009 2.00e-02 2.50e+03 1.73e-02 3.00e+00 pdb=" C ASP A 197 " -0.030 2.00e-02 2.50e+03 pdb=" O ASP A 197 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS A 198 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 563 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C ARG A 563 " -0.029 2.00e-02 2.50e+03 pdb=" O ARG A 563 " 0.011 2.00e-02 2.50e+03 pdb=" N PRO A 564 " 0.010 2.00e-02 2.50e+03 ... (remaining 1540 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1916 2.80 - 3.33: 8067 3.33 - 3.85: 14185 3.85 - 4.38: 17461 4.38 - 4.90: 28435 Nonbonded interactions: 70064 Sorted by model distance: nonbonded pdb=" OD2 ASP A 23 " pdb="ZN ZN A1203 " model vdw 2.280 2.230 nonbonded pdb=" O PHE A 925 " pdb=" ND1 HIS A 928 " model vdw 2.372 2.520 nonbonded pdb=" ND2 ASN A 15 " pdb=" O GLY A 44 " model vdw 2.379 2.520 nonbonded pdb=" OD1 ASP A 842 " pdb=" N VAL A 843 " model vdw 2.481 2.520 nonbonded pdb=" O ALA A 112 " pdb=" OH TYR A 296 " model vdw 2.483 2.440 ... (remaining 70059 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=0.00 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: 0.680 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: 0.000 Extract box with map and model: 3.820 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 31.650 Find NCS groups from input model: 0.210 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:11.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 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 : 0.008 0.154 9246 Z= 0.508 Angle : 1.335 11.191 12681 Z= 0.916 Chirality : 0.107 0.459 1402 Planarity : 0.005 0.027 1543 Dihedral : 16.901 113.218 3573 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.28 % Allowed : 8.59 % Favored : 90.13 % Cbeta Deviations : 0.20 % 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: -1.39 (0.22), residues: 1066 helix: -0.50 (0.20), residues: 474 sheet: 0.14 (0.60), residues: 68 loop : -1.42 (0.23), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 561 HIS 0.006 0.002 HIS A 48 PHE 0.021 0.003 PHE A 850 TYR 0.021 0.003 TYR A 392 ARG 0.006 0.001 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 0.931 Fit side-chains REVERT: A 196 MET cc_start: 0.8573 (ptm) cc_final: 0.8290 (ptm) REVERT: A 197 ASP cc_start: 0.8560 (t0) cc_final: 0.8283 (t0) REVERT: A 622 LYS cc_start: 0.7930 (tppt) cc_final: 0.7714 (ttpp) REVERT: A 793 MET cc_start: 0.8507 (tpt) cc_final: 0.8239 (tpt) REVERT: A 968 VAL cc_start: 0.8275 (t) cc_final: 0.7696 (t) outliers start: 11 outliers final: 2 residues processed: 128 average time/residue: 1.3868 time to fit residues: 188.1872 Evaluate side-chains 61 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 927 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 0.0070 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 HIS A 273 GLN A 687 GLN A 855 GLN A 993 HIS A1063 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9246 Z= 0.217 Angle : 0.616 6.740 12681 Z= 0.338 Chirality : 0.045 0.221 1402 Planarity : 0.005 0.046 1543 Dihedral : 15.825 108.108 1631 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.02 % Allowed : 12.66 % Favored : 84.32 % 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: -0.20 (0.24), residues: 1066 helix: 0.98 (0.22), residues: 501 sheet: -0.09 (0.49), residues: 92 loop : -1.37 (0.24), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 561 HIS 0.004 0.001 HIS A1063 PHE 0.017 0.001 PHE A 754 TYR 0.033 0.002 TYR A 666 ARG 0.006 0.001 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 71 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.7656 (mtm110) cc_final: 0.7308 (mtm110) REVERT: A 95 LYS cc_start: 0.7700 (tmmt) cc_final: 0.7434 (tptp) REVERT: A 524 ARG cc_start: 0.7473 (ttp-110) cc_final: 0.7074 (ttp-110) REVERT: A 756 ASP cc_start: 0.7698 (t0) cc_final: 0.7449 (t0) REVERT: A 1074 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7130 (m-30) outliers start: 26 outliers final: 8 residues processed: 90 average time/residue: 1.1284 time to fit residues: 109.5843 Evaluate side-chains 59 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 1074 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9246 Z= 0.266 Angle : 0.599 11.839 12681 Z= 0.325 Chirality : 0.044 0.213 1402 Planarity : 0.005 0.054 1543 Dihedral : 15.553 102.993 1631 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.83 % Allowed : 14.87 % Favored : 81.30 % 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 (0.24), residues: 1066 helix: 1.03 (0.23), residues: 506 sheet: -1.05 (0.47), residues: 104 loop : -1.28 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 561 HIS 0.005 0.001 HIS A 323 PHE 0.014 0.002 PHE A 754 TYR 0.015 0.002 TYR A 666 ARG 0.004 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 59 time to evaluate : 1.108 Fit side-chains revert: symmetry clash REVERT: A 21 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.7592 (mtm) REVERT: A 85 ARG cc_start: 0.7781 (mtm110) cc_final: 0.7300 (mtm180) REVERT: A 756 ASP cc_start: 0.7691 (t0) cc_final: 0.7481 (t0) outliers start: 33 outliers final: 16 residues processed: 83 average time/residue: 1.0193 time to fit residues: 92.1308 Evaluate side-chains 72 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 55 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 670 PRO Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 927 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.0870 chunk 74 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 66 optimal weight: 0.0060 chunk 99 optimal weight: 0.0020 chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9246 Z= 0.155 Angle : 0.514 10.198 12681 Z= 0.276 Chirality : 0.041 0.201 1402 Planarity : 0.004 0.052 1543 Dihedral : 15.220 96.168 1631 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.02 % Allowed : 15.21 % Favored : 81.77 % 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: 0.05 (0.25), residues: 1066 helix: 1.30 (0.23), residues: 508 sheet: -1.04 (0.45), residues: 109 loop : -1.14 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 561 HIS 0.002 0.000 HIS A 323 PHE 0.014 0.001 PHE A 754 TYR 0.014 0.001 TYR A 781 ARG 0.003 0.000 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 63 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 524 ARG cc_start: 0.7431 (ttp-110) cc_final: 0.6908 (ttp-110) REVERT: A 750 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7221 (mp0) REVERT: A 756 ASP cc_start: 0.7703 (t0) cc_final: 0.7497 (t0) REVERT: A 967 LYS cc_start: 0.7346 (tppt) cc_final: 0.6980 (tppp) outliers start: 26 outliers final: 14 residues processed: 81 average time/residue: 1.1127 time to fit residues: 97.7549 Evaluate side-chains 69 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 55 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 965 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 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 198 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9246 Z= 0.398 Angle : 0.652 10.663 12681 Z= 0.350 Chirality : 0.048 0.251 1402 Planarity : 0.005 0.052 1543 Dihedral : 15.520 92.666 1631 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.83 % Allowed : 16.38 % Favored : 79.79 % 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: -0.54 (0.24), residues: 1066 helix: 0.77 (0.23), residues: 506 sheet: -1.40 (0.46), residues: 102 loop : -1.37 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 561 HIS 0.007 0.002 HIS A 323 PHE 0.017 0.002 PHE A 850 TYR 0.018 0.002 TYR A 625 ARG 0.004 0.001 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 56 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: A 21 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.7727 (mtm) REVERT: A 196 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8137 (ptm) REVERT: A 490 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.5297 (mtt) REVERT: A 586 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7701 (mtt) REVERT: A 751 PHE cc_start: 0.7214 (t80) cc_final: 0.7012 (t80) outliers start: 33 outliers final: 16 residues processed: 81 average time/residue: 1.0407 time to fit residues: 92.1833 Evaluate side-chains 74 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 54 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 965 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 chunk 55 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 877 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9246 Z= 0.214 Angle : 0.551 10.878 12681 Z= 0.295 Chirality : 0.043 0.235 1402 Planarity : 0.004 0.054 1543 Dihedral : 15.238 86.491 1631 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.95 % Allowed : 16.96 % Favored : 79.09 % 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: -0.30 (0.25), residues: 1066 helix: 1.02 (0.23), residues: 510 sheet: -1.41 (0.43), residues: 109 loop : -1.29 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 561 HIS 0.004 0.001 HIS A 323 PHE 0.011 0.001 PHE A 754 TYR 0.015 0.002 TYR A 989 ARG 0.003 0.000 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 56 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 40 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8024 (mtt) REVERT: A 85 ARG cc_start: 0.8239 (mtp180) cc_final: 0.7592 (ptt180) REVERT: A 196 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8173 (ptm) REVERT: A 490 MET cc_start: 0.7020 (OUTLIER) cc_final: 0.5138 (mtt) REVERT: A 586 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7659 (mtt) REVERT: A 967 LYS cc_start: 0.7374 (tppt) cc_final: 0.7003 (tppp) outliers start: 34 outliers final: 16 residues processed: 82 average time/residue: 1.0107 time to fit residues: 90.3658 Evaluate side-chains 78 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 58 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 965 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 877 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9246 Z= 0.350 Angle : 0.624 10.779 12681 Z= 0.335 Chirality : 0.046 0.251 1402 Planarity : 0.005 0.053 1543 Dihedral : 15.400 77.601 1631 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.37 % Allowed : 18.00 % Favored : 78.63 % 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: -0.61 (0.24), residues: 1066 helix: 0.73 (0.23), residues: 506 sheet: -1.42 (0.46), residues: 102 loop : -1.43 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 561 HIS 0.007 0.001 HIS A 323 PHE 0.016 0.002 PHE A 850 TYR 0.016 0.002 TYR A 989 ARG 0.003 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 60 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 21 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.7660 (mtm) REVERT: A 40 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8181 (mtt) REVERT: A 85 ARG cc_start: 0.8260 (mtp180) cc_final: 0.7627 (ptt180) REVERT: A 196 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8111 (ptm) REVERT: A 490 MET cc_start: 0.6986 (OUTLIER) cc_final: 0.5117 (mtt) REVERT: A 586 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7689 (mtt) REVERT: A 967 LYS cc_start: 0.7300 (tppt) cc_final: 0.6989 (tppp) REVERT: A 970 ASP cc_start: 0.7032 (m-30) cc_final: 0.6719 (p0) outliers start: 29 outliers final: 17 residues processed: 82 average time/residue: 1.0660 time to fit residues: 94.8091 Evaluate side-chains 79 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 57 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 965 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 91 optimal weight: 9.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9246 Z= 0.170 Angle : 0.544 12.911 12681 Z= 0.288 Chirality : 0.042 0.267 1402 Planarity : 0.004 0.050 1543 Dihedral : 15.145 68.536 1631 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.14 % Allowed : 18.47 % Favored : 78.40 % 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: -0.23 (0.25), residues: 1066 helix: 1.07 (0.23), residues: 510 sheet: -1.37 (0.44), residues: 110 loop : -1.24 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 561 HIS 0.003 0.001 HIS A 323 PHE 0.008 0.001 PHE A 475 TYR 0.017 0.001 TYR A 989 ARG 0.004 0.000 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 61 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.8183 (mtp180) cc_final: 0.7568 (ptt180) REVERT: A 196 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8139 (ptm) REVERT: A 490 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.4916 (mtt) REVERT: A 612 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7480 (mp) REVERT: A 844 ASN cc_start: 0.7462 (OUTLIER) cc_final: 0.6797 (p0) REVERT: A 967 LYS cc_start: 0.7424 (tppt) cc_final: 0.7113 (tppp) REVERT: A 970 ASP cc_start: 0.7093 (m-30) cc_final: 0.6830 (p0) REVERT: A 1074 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7388 (m-30) outliers start: 27 outliers final: 17 residues processed: 82 average time/residue: 1.0766 time to fit residues: 95.7571 Evaluate side-chains 81 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 59 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 844 ASN Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1074 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 877 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9246 Z= 0.215 Angle : 0.566 15.213 12681 Z= 0.296 Chirality : 0.043 0.236 1402 Planarity : 0.004 0.050 1543 Dihedral : 15.139 60.984 1631 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.25 % Allowed : 18.47 % Favored : 78.28 % 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: -0.22 (0.25), residues: 1066 helix: 1.07 (0.23), residues: 510 sheet: -1.38 (0.44), residues: 110 loop : -1.22 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 561 HIS 0.004 0.001 HIS A 323 PHE 0.010 0.001 PHE A 475 TYR 0.019 0.001 TYR A 989 ARG 0.005 0.000 ARG A 416 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 57 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.8202 (mtp180) cc_final: 0.7589 (ptt180) REVERT: A 196 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8124 (ptm) REVERT: A 490 MET cc_start: 0.6893 (OUTLIER) cc_final: 0.5073 (mtt) REVERT: A 612 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7510 (mp) REVERT: A 844 ASN cc_start: 0.7500 (OUTLIER) cc_final: 0.6882 (p0) REVERT: A 967 LYS cc_start: 0.7373 (tppt) cc_final: 0.7061 (tppp) REVERT: A 970 ASP cc_start: 0.6991 (m-30) cc_final: 0.6726 (p0) REVERT: A 1074 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7355 (m-30) outliers start: 28 outliers final: 18 residues processed: 79 average time/residue: 1.0133 time to fit residues: 87.4402 Evaluate side-chains 80 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 57 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 844 ASN Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1074 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 chunk 26 optimal weight: 0.4980 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 877 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 9246 Z= 0.372 Angle : 0.660 17.830 12681 Z= 0.346 Chirality : 0.047 0.239 1402 Planarity : 0.005 0.052 1543 Dihedral : 15.356 59.864 1631 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.02 % Allowed : 18.47 % Favored : 78.51 % 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: -0.57 (0.24), residues: 1066 helix: 0.76 (0.23), residues: 505 sheet: -1.40 (0.46), residues: 102 loop : -1.41 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 561 HIS 0.007 0.001 HIS A 323 PHE 0.018 0.002 PHE A 850 TYR 0.020 0.002 TYR A 989 ARG 0.005 0.001 ARG A 416 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 55 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 85 ARG cc_start: 0.8218 (mtp180) cc_final: 0.7607 (ptt180) REVERT: A 196 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8192 (ptm) REVERT: A 416 ARG cc_start: 0.7274 (mtm-85) cc_final: 0.6596 (mtt180) REVERT: A 490 MET cc_start: 0.6952 (OUTLIER) cc_final: 0.5183 (mtt) REVERT: A 586 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7676 (mtt) REVERT: A 612 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7602 (mp) REVERT: A 697 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6913 (tm-30) REVERT: A 844 ASN cc_start: 0.7615 (OUTLIER) cc_final: 0.6968 (p0) REVERT: A 967 LYS cc_start: 0.7347 (tppt) cc_final: 0.7015 (tppp) REVERT: A 970 ASP cc_start: 0.7018 (m-30) cc_final: 0.6768 (p0) REVERT: A 1074 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7266 (m-30) outliers start: 26 outliers final: 17 residues processed: 77 average time/residue: 1.0831 time to fit residues: 90.6877 Evaluate side-chains 79 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 55 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 844 ASN Chi-restraints excluded: chain A residue 915 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1074 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.110492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.088090 restraints weight = 15124.860| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.98 r_work: 0.3094 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9246 Z= 0.195 Angle : 0.578 18.848 12681 Z= 0.299 Chirality : 0.042 0.203 1402 Planarity : 0.004 0.051 1543 Dihedral : 15.110 59.711 1631 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.90 % Allowed : 18.82 % Favored : 78.28 % 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: -0.28 (0.25), residues: 1066 helix: 1.02 (0.23), residues: 510 sheet: -1.40 (0.44), residues: 110 loop : -1.25 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 561 HIS 0.004 0.001 HIS A 323 PHE 0.009 0.001 PHE A 475 TYR 0.021 0.001 TYR A 989 ARG 0.004 0.000 ARG A 416 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2630.57 seconds wall clock time: 47 minutes 44.02 seconds (2864.02 seconds total)