Starting phenix.real_space_refine on Thu Mar 14 18:17:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avy_15687/03_2024/8avy_15687.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avy_15687/03_2024/8avy_15687.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/8avy_15687/03_2024/8avy_15687.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avy_15687/03_2024/8avy_15687.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avy_15687/03_2024/8avy_15687.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8avy_15687/03_2024/8avy_15687.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= 0.044 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 P 6 5.49 5 Mg 2 5.21 5 S 31 5.16 5 C 6116 2.51 5 N 1552 2.21 5 O 1726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9433 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9085 Classifications: {'peptide': 1175} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 29, 'TRANS': 1145} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 348 Unusual residues: {' MG': 2, 'ATP': 2, 'Y01': 8} Classifications: {'undetermined': 12, 'water': 4} Link IDs: {None: 15} Time building chain proxies: 5.38, per 1000 atoms: 0.57 Number of scatterers: 9433 At special positions: 0 Unit cell: (72.819, 87.048, 148.986, 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) S 31 16.00 P 6 15.00 Mg 2 11.99 O 1726 8.00 N 1552 7.00 C 6116 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: 3.90 Conformation dependent library (CDL) restraints added in 1.7 seconds 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 71.1% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 43 through 62 Processing helix chain 'A' and resid 62 through 73 Processing helix chain 'A' and resid 74 through 85 Processing helix chain 'A' and resid 91 through 154 removed outlier: 3.891A pdb=" N ARG A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP A 132 " --> pdb=" O GLN A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 164 through 180 removed outlier: 3.882A pdb=" N THR A 172 " --> pdb=" O ASN A 168 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 207 removed outlier: 3.900A pdb=" N GLY A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 256 Proline residue: A 219 - end of helix Processing helix chain 'A' and resid 256 through 263 Processing helix chain 'A' and resid 265 through 319 removed outlier: 3.545A pdb=" N ASN A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 335 through 367 removed outlier: 4.486A pdb=" N PHE A 339 " --> pdb=" O CYS A 335 " (cutoff:3.500A) Proline residue: A 346 - end of helix removed outlier: 3.662A pdb=" N TYR A 359 " --> pdb=" O ARG A 355 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N GLU A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 437 Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 479 through 486 Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 505 through 511 Processing helix chain 'A' and resid 514 through 518 Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 528 through 543 removed outlier: 4.028A pdb=" N ARG A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 571 removed outlier: 3.541A pdb=" N VAL A 564 " --> pdb=" O GLU A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 576 removed outlier: 3.638A pdb=" N GLY A 575 " --> pdb=" O ALA A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 590 removed outlier: 4.047A pdb=" N VAL A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASN A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 584 through 590' Processing helix chain 'A' and resid 607 through 615 Processing helix chain 'A' and resid 616 through 623 Processing helix chain 'A' and resid 691 through 698 Processing helix chain 'A' and resid 699 through 702 removed outlier: 4.914A pdb=" N THR A 702 " --> pdb=" O LEU A 699 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 699 through 702' Processing helix chain 'A' and resid 703 through 737 removed outlier: 3.797A pdb=" N GLN A 721 " --> pdb=" O ASN A 717 " (cutoff:3.500A) Proline residue: A 722 - end of helix removed outlier: 4.237A pdb=" N SER A 725 " --> pdb=" O GLN A 721 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 726 " --> pdb=" O PRO A 722 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL A 734 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASN A 737 " --> pdb=" O GLY A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 743 No H-bonds generated for 'chain 'A' and resid 741 through 743' Processing helix chain 'A' and resid 744 through 795 removed outlier: 3.675A pdb=" N PHE A 773 " --> pdb=" O GLN A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 801 removed outlier: 3.516A pdb=" N PHE A 800 " --> pdb=" O ASP A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 805 Processing helix chain 'A' and resid 806 through 823 removed outlier: 4.163A pdb=" N ALA A 818 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA A 819 " --> pdb=" O ALA A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 850 Processing helix chain 'A' and resid 852 through 899 removed outlier: 3.852A pdb=" N LEU A 856 " --> pdb=" O GLN A 852 " (cutoff:3.500A) Proline residue: A 862 - end of helix removed outlier: 3.625A pdb=" N ALA A 867 " --> pdb=" O ILE A 863 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS A 881 " --> pdb=" O GLY A 877 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 887 " --> pdb=" O LYS A 883 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY A 888 " --> pdb=" O LYS A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 906 Processing helix chain 'A' and resid 908 through 920 Processing helix chain 'A' and resid 920 through 962 removed outlier: 3.621A pdb=" N HIS A 932 " --> pdb=" O MET A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 989 removed outlier: 3.573A pdb=" N PHE A 979 " --> pdb=" O SER A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1010 removed outlier: 3.866A pdb=" N LYS A 996 " --> pdb=" O PRO A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1080 removed outlier: 3.810A pdb=" N VAL A1076 " --> pdb=" O LYS A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1107 Processing helix chain 'A' and resid 1122 through 1129 Processing helix chain 'A' and resid 1137 through 1148 Processing helix chain 'A' and resid 1150 through 1156 Processing helix chain 'A' and resid 1159 through 1163 Processing helix chain 'A' and resid 1166 through 1170 Processing helix chain 'A' and resid 1173 through 1187 Processing helix chain 'A' and resid 1203 through 1217 Processing helix chain 'A' and resid 1229 through 1233 removed outlier: 3.554A pdb=" N THR A1232 " --> pdb=" O ARG A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1259 Processing helix chain 'A' and resid 1261 through 1267 removed outlier: 3.565A pdb=" N VAL A1267 " --> pdb=" O TYR A1263 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 406 through 413 removed outlier: 6.859A pdb=" N LYS A 407 " --> pdb=" O HIS A 394 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N HIS A 394 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU A 409 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N PHE A 390 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N SER A 448 " --> pdb=" O PHE A 390 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ASN A 392 " --> pdb=" O MET A 446 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N MET A 446 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 466 through 469 removed outlier: 6.691A pdb=" N GLY A 467 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ASP A 551 " --> pdb=" O GLY A 467 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL A 469 " --> pdb=" O ASP A 551 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU A 548 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE A 581 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU A 550 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL A 419 " --> pdb=" O VAL A 580 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR A 418 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ALA A 595 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ALA A 420 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N PHE A 597 " --> pdb=" O ALA A 420 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL A 422 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU A 604 " --> pdb=" O GLY A 596 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1053 through 1056 removed outlier: 5.626A pdb=" N PHE A1033 " --> pdb=" O PHE A1091 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N PHE A1091 " --> pdb=" O PHE A1033 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLY A1035 " --> pdb=" O SER A1089 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N SER A1089 " --> pdb=" O GLY A1035 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1109 through 1112 removed outlier: 6.233A pdb=" N GLY A1110 " --> pdb=" O LEU A1194 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ASP A1196 " --> pdb=" O GLY A1110 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL A1112 " --> pdb=" O ASP A1196 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU A1193 " --> pdb=" O ILE A1224 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE A1226 " --> pdb=" O LEU A1193 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU A1195 " --> pdb=" O ILE A1226 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N THR A1061 " --> pdb=" O LEU A1238 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL A1240 " --> pdb=" O THR A1061 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ALA A1063 " --> pdb=" O VAL A1240 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE A1242 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL A1065 " --> pdb=" O ILE A1242 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLN A1243 " --> pdb=" O VAL A1247 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL A1247 " --> pdb=" O GLN A1243 " (cutoff:3.500A) 614 hydrogen bonds defined for protein. 1791 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.46 Time building geometry restraints manager: 3.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1517 1.30 - 1.42: 2378 1.42 - 1.55: 5636 1.55 - 1.68: 31 1.68 - 1.81: 61 Bond restraints: 9623 Sorted by residual: bond pdb=" CA ALA A 56 " pdb=" CB ALA A 56 " ideal model delta sigma weight residual 1.528 1.440 0.089 1.56e-02 4.11e+03 3.25e+01 bond pdb=" C TRP A 132 " pdb=" O TRP A 132 " ideal model delta sigma weight residual 1.236 1.167 0.069 1.29e-02 6.01e+03 2.90e+01 bond pdb=" CA ALA A 125 " pdb=" CB ALA A 125 " ideal model delta sigma weight residual 1.528 1.449 0.079 1.59e-02 3.96e+03 2.47e+01 bond pdb=" CA SER A 130 " pdb=" CB SER A 130 " ideal model delta sigma weight residual 1.529 1.454 0.075 1.55e-02 4.16e+03 2.33e+01 bond pdb=" C PHE A 131 " pdb=" O PHE A 131 " ideal model delta sigma weight residual 1.237 1.180 0.057 1.19e-02 7.06e+03 2.27e+01 ... (remaining 9618 not shown) Histogram of bond angle deviations from ideal: 98.18 - 106.75: 260 106.75 - 115.32: 5966 115.32 - 123.88: 6630 123.88 - 132.45: 199 132.45 - 141.02: 17 Bond angle restraints: 13072 Sorted by residual: angle pdb=" N THR A 37 " pdb=" CA THR A 37 " pdb=" C THR A 37 " ideal model delta sigma weight residual 111.40 100.68 10.72 1.22e+00 6.72e-01 7.73e+01 angle pdb=" C PHE A 131 " pdb=" CA PHE A 131 " pdb=" CB PHE A 131 " ideal model delta sigma weight residual 110.85 121.06 -10.21 1.70e+00 3.46e-01 3.61e+01 angle pdb=" C THR A 54 " pdb=" CA THR A 54 " pdb=" CB THR A 54 " ideal model delta sigma weight residual 110.85 120.04 -9.19 1.70e+00 3.46e-01 2.92e+01 angle pdb=" C PHE A 197 " pdb=" CA PHE A 197 " pdb=" CB PHE A 197 " ideal model delta sigma weight residual 110.85 119.70 -8.85 1.70e+00 3.46e-01 2.71e+01 angle pdb=" C THR A 37 " pdb=" CA THR A 37 " pdb=" CB THR A 37 " ideal model delta sigma weight residual 110.79 119.50 -8.71 1.68e+00 3.54e-01 2.69e+01 ... (remaining 13067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.46: 5843 24.46 - 48.91: 234 48.91 - 73.37: 40 73.37 - 97.82: 20 97.82 - 122.28: 5 Dihedral angle restraints: 6142 sinusoidal: 2777 harmonic: 3365 Sorted by residual: dihedral pdb=" C THR A 54 " pdb=" N THR A 54 " pdb=" CA THR A 54 " pdb=" CB THR A 54 " ideal model delta harmonic sigma weight residual -122.00 -135.00 13.00 0 2.50e+00 1.60e-01 2.70e+01 dihedral pdb=" C PHE A 190 " pdb=" N PHE A 190 " pdb=" CA PHE A 190 " pdb=" CB PHE A 190 " ideal model delta harmonic sigma weight residual -122.60 -134.15 11.55 0 2.50e+00 1.60e-01 2.13e+01 dihedral pdb=" C PHE A 197 " pdb=" N PHE A 197 " pdb=" CA PHE A 197 " pdb=" CB PHE A 197 " ideal model delta harmonic sigma weight residual -122.60 -133.22 10.62 0 2.50e+00 1.60e-01 1.80e+01 ... (remaining 6139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1394 0.082 - 0.163: 102 0.163 - 0.245: 8 0.245 - 0.327: 4 0.327 - 0.409: 5 Chirality restraints: 1513 Sorted by residual: chirality pdb=" CA THR A 54 " pdb=" N THR A 54 " pdb=" C THR A 54 " pdb=" CB THR A 54 " both_signs ideal model delta sigma weight residual False 2.53 2.12 0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CB VAL A 124 " pdb=" CA VAL A 124 " pdb=" CG1 VAL A 124 " pdb=" CG2 VAL A 124 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CBB Y01 A2009 " pdb=" CAC Y01 A2009 " pdb=" CAO Y01 A2009 " pdb=" CBE Y01 A2009 " both_signs ideal model delta sigma weight residual False 2.58 2.20 0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 1510 not shown) Planarity restraints: 1610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 34 " -0.028 2.00e-02 2.50e+03 5.48e-02 3.00e+01 pdb=" C SER A 34 " 0.095 2.00e-02 2.50e+03 pdb=" O SER A 34 " -0.035 2.00e-02 2.50e+03 pdb=" N VAL A 35 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP A2001 " 0.046 2.00e-02 2.50e+03 2.08e-02 1.19e+01 pdb=" C2 ATP A2001 " -0.006 2.00e-02 2.50e+03 pdb=" C4 ATP A2001 " -0.016 2.00e-02 2.50e+03 pdb=" C5 ATP A2001 " -0.011 2.00e-02 2.50e+03 pdb=" C6 ATP A2001 " -0.003 2.00e-02 2.50e+03 pdb=" C8 ATP A2001 " 0.008 2.00e-02 2.50e+03 pdb=" N1 ATP A2001 " 0.014 2.00e-02 2.50e+03 pdb=" N3 ATP A2001 " -0.010 2.00e-02 2.50e+03 pdb=" N6 ATP A2001 " 0.025 2.00e-02 2.50e+03 pdb=" N7 ATP A2001 " -0.015 2.00e-02 2.50e+03 pdb=" N9 ATP A2001 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 37 " -0.016 2.00e-02 2.50e+03 3.34e-02 1.11e+01 pdb=" C THR A 37 " 0.058 2.00e-02 2.50e+03 pdb=" O THR A 37 " -0.022 2.00e-02 2.50e+03 pdb=" N MET A 38 " -0.019 2.00e-02 2.50e+03 ... (remaining 1607 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 69 2.59 - 3.17: 8034 3.17 - 3.74: 15125 3.74 - 4.32: 21496 4.32 - 4.90: 34891 Nonbonded interactions: 79615 Sorted by model distance: nonbonded pdb=" O3G ATP A2003 " pdb="MG MG A2004 " model vdw 2.008 2.170 nonbonded pdb="MG MG A2004 " pdb=" O HOH A2101 " model vdw 2.009 2.170 nonbonded pdb="MG MG A2002 " pdb=" O HOH A2102 " model vdw 2.059 2.170 nonbonded pdb=" OG SER A 430 " pdb="MG MG A2002 " model vdw 2.072 2.170 nonbonded pdb="MG MG A2002 " pdb=" O HOH A2103 " model vdw 2.077 2.170 ... (remaining 79610 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 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: 5.130 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.280 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 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 0.089 9623 Z= 0.341 Angle : 0.777 10.724 13072 Z= 0.496 Chirality : 0.052 0.409 1513 Planarity : 0.004 0.055 1610 Dihedral : 14.562 122.279 3986 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.74 % Allowed : 6.93 % Favored : 92.33 % Cbeta Deviations : 0.37 % 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: 1.35 (0.24), residues: 1171 helix: 1.46 (0.19), residues: 790 sheet: 0.76 (0.64), residues: 60 loop : -0.38 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 228 HIS 0.007 0.001 HIS A 60 PHE 0.027 0.002 PHE A 131 TYR 0.018 0.002 TYR A 49 ARG 0.003 0.000 ARG A 400 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 161 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 ASN cc_start: 0.7805 (m110) cc_final: 0.7501 (m-40) REVERT: A 848 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7994 (mp) REVERT: A 1243 GLN cc_start: 0.7920 (tt0) cc_final: 0.7697 (tp40) outliers start: 7 outliers final: 4 residues processed: 167 average time/residue: 1.1778 time to fit residues: 211.0395 Evaluate side-chains 118 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 113 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1267 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 0.0870 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 ASN A 717 ASN ** A 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 GLN A1244 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9623 Z= 0.263 Angle : 0.598 10.748 13072 Z= 0.296 Chirality : 0.043 0.207 1513 Planarity : 0.004 0.035 1610 Dihedral : 11.800 87.720 1904 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.47 % Allowed : 12.39 % Favored : 84.14 % 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: 1.41 (0.24), residues: 1171 helix: 1.51 (0.18), residues: 797 sheet: 0.82 (0.63), residues: 60 loop : -0.43 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 228 HIS 0.004 0.001 HIS A 141 PHE 0.025 0.002 PHE A 508 TYR 0.031 0.002 TYR A 306 ARG 0.003 0.000 ARG A 908 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 123 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7977 (mtm-85) cc_final: 0.7629 (mtt90) REVERT: A 293 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8397 (tt) REVERT: A 424 ASN cc_start: 0.7895 (m110) cc_final: 0.7576 (m-40) REVERT: A 802 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7240 (t70) REVERT: A 915 MET cc_start: 0.8732 (mtm) cc_final: 0.8463 (mtp) REVERT: A 1054 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8192 (pp) REVERT: A 1159 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7338 (t0) REVERT: A 1211 GLN cc_start: 0.8081 (tp-100) cc_final: 0.7331 (tm-30) REVERT: A 1223 VAL cc_start: 0.8999 (p) cc_final: 0.8688 (t) outliers start: 33 outliers final: 16 residues processed: 141 average time/residue: 1.0578 time to fit residues: 161.4330 Evaluate side-chains 134 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 114 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 948 SER Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1267 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 88 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 154 GLN ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1244 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9623 Z= 0.337 Angle : 0.591 9.606 13072 Z= 0.298 Chirality : 0.043 0.207 1513 Planarity : 0.004 0.036 1610 Dihedral : 10.916 87.536 1902 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.36 % Allowed : 12.82 % Favored : 83.82 % 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: 1.25 (0.24), residues: 1171 helix: 1.40 (0.18), residues: 795 sheet: 0.81 (0.65), residues: 58 loop : -0.50 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 228 HIS 0.005 0.001 HIS A 141 PHE 0.026 0.002 PHE A 508 TYR 0.035 0.002 TYR A 306 ARG 0.003 0.000 ARG A 908 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 124 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8004 (mtm-85) cc_final: 0.7623 (mtt90) REVERT: A 293 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8457 (tt) REVERT: A 404 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7865 (mt0) REVERT: A 424 ASN cc_start: 0.7852 (m110) cc_final: 0.7529 (m-40) REVERT: A 802 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7198 (t70) REVERT: A 848 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7992 (mp) REVERT: A 915 MET cc_start: 0.8729 (mtm) cc_final: 0.8412 (mtp) REVERT: A 1159 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7350 (t0) REVERT: A 1208 LYS cc_start: 0.7916 (ttpt) cc_final: 0.7552 (mtpp) REVERT: A 1211 GLN cc_start: 0.8161 (tp-100) cc_final: 0.7415 (tm-30) REVERT: A 1223 VAL cc_start: 0.9056 (OUTLIER) cc_final: 0.8789 (t) outliers start: 32 outliers final: 16 residues processed: 142 average time/residue: 1.1268 time to fit residues: 172.8260 Evaluate side-chains 137 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 115 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 508 PHE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 948 SER Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1267 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 0.4980 chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 0.0970 chunk 11 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9623 Z= 0.166 Angle : 0.512 8.652 13072 Z= 0.258 Chirality : 0.040 0.203 1513 Planarity : 0.003 0.035 1610 Dihedral : 9.961 89.164 1902 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.94 % Allowed : 14.08 % Favored : 82.98 % 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: 1.59 (0.24), residues: 1171 helix: 1.70 (0.18), residues: 797 sheet: 0.85 (0.65), residues: 58 loop : -0.49 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 228 HIS 0.002 0.001 HIS A 141 PHE 0.014 0.001 PHE A 508 TYR 0.031 0.001 TYR A 306 ARG 0.002 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 115 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7965 (mtm-85) cc_final: 0.7592 (mtt90) REVERT: A 293 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8396 (tt) REVERT: A 424 ASN cc_start: 0.7868 (m110) cc_final: 0.7548 (m-40) REVERT: A 802 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7199 (t70) REVERT: A 848 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7984 (mp) REVERT: A 915 MET cc_start: 0.8679 (mtm) cc_final: 0.8406 (mtp) REVERT: A 1208 LYS cc_start: 0.7887 (ttpt) cc_final: 0.7282 (pttm) REVERT: A 1211 GLN cc_start: 0.8137 (tp-100) cc_final: 0.7432 (tm-30) outliers start: 28 outliers final: 15 residues processed: 133 average time/residue: 1.2109 time to fit residues: 173.2825 Evaluate side-chains 128 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 948 SER Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1243 GLN Chi-restraints excluded: chain A residue 1267 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 96 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 28 optimal weight: 20.0000 chunk 38 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 ASN ** A 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9623 Z= 0.198 Angle : 0.511 8.754 13072 Z= 0.259 Chirality : 0.040 0.198 1513 Planarity : 0.003 0.035 1610 Dihedral : 9.689 89.759 1900 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.57 % Allowed : 14.39 % Favored : 82.04 % 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: 1.63 (0.24), residues: 1171 helix: 1.73 (0.18), residues: 797 sheet: 0.74 (0.63), residues: 60 loop : -0.48 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 228 HIS 0.003 0.001 HIS A 141 PHE 0.020 0.001 PHE A 508 TYR 0.030 0.001 TYR A 306 ARG 0.002 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 115 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7975 (mtm-85) cc_final: 0.7598 (mtt90) REVERT: A 293 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8419 (tt) REVERT: A 404 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7804 (mt0) REVERT: A 424 ASN cc_start: 0.7870 (m110) cc_final: 0.7543 (m-40) REVERT: A 802 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7201 (t70) REVERT: A 848 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.8025 (mp) REVERT: A 1159 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7255 (t0) REVERT: A 1208 LYS cc_start: 0.7892 (ttpt) cc_final: 0.7477 (mtpp) REVERT: A 1211 GLN cc_start: 0.8165 (tp-100) cc_final: 0.7499 (tm-30) outliers start: 34 outliers final: 17 residues processed: 136 average time/residue: 1.1418 time to fit residues: 167.3184 Evaluate side-chains 131 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 884 LYS Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1243 GLN Chi-restraints excluded: chain A residue 1267 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 113 optimal weight: 0.0060 chunk 93 optimal weight: 0.4980 chunk 52 optimal weight: 0.0980 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 109 optimal weight: 0.0070 overall best weight: 0.3014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9623 Z= 0.119 Angle : 0.468 9.444 13072 Z= 0.238 Chirality : 0.038 0.193 1513 Planarity : 0.003 0.035 1610 Dihedral : 9.162 82.303 1900 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.84 % Allowed : 15.34 % Favored : 81.83 % 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: 1.93 (0.24), residues: 1171 helix: 1.97 (0.18), residues: 798 sheet: 0.78 (0.64), residues: 60 loop : -0.39 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 228 HIS 0.002 0.000 HIS A 608 PHE 0.016 0.001 PHE A 934 TYR 0.027 0.001 TYR A 306 ARG 0.002 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 116 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7953 (mtm-85) cc_final: 0.7647 (mtt90) REVERT: A 293 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8351 (tt) REVERT: A 424 ASN cc_start: 0.7873 (m110) cc_final: 0.7544 (m-40) REVERT: A 802 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7218 (t70) REVERT: A 848 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.8054 (mp) REVERT: A 1208 LYS cc_start: 0.7841 (ttpt) cc_final: 0.7251 (pttm) REVERT: A 1211 GLN cc_start: 0.8122 (tp-100) cc_final: 0.7495 (tm-30) outliers start: 27 outliers final: 12 residues processed: 132 average time/residue: 1.1537 time to fit residues: 163.9104 Evaluate side-chains 127 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 944 MET Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1243 GLN Chi-restraints excluded: chain A residue 1267 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.8980 chunk 64 optimal weight: 0.4980 chunk 82 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 52 optimal weight: 0.0470 chunk 69 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 ASN ** A 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 9623 Z= 0.151 Angle : 0.485 11.911 13072 Z= 0.247 Chirality : 0.039 0.192 1513 Planarity : 0.003 0.035 1610 Dihedral : 9.080 81.216 1899 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.63 % Allowed : 15.76 % Favored : 81.62 % 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: 1.99 (0.24), residues: 1171 helix: 2.03 (0.18), residues: 797 sheet: 0.63 (0.63), residues: 60 loop : -0.36 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 228 HIS 0.002 0.000 HIS A 141 PHE 0.018 0.001 PHE A 934 TYR 0.029 0.001 TYR A 306 ARG 0.002 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7950 (mtm-85) cc_final: 0.7636 (mtt90) REVERT: A 404 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7773 (mt0) REVERT: A 424 ASN cc_start: 0.7875 (m110) cc_final: 0.7541 (m-40) REVERT: A 802 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7178 (t70) REVERT: A 848 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.8037 (mp) REVERT: A 915 MET cc_start: 0.8698 (mtm) cc_final: 0.8418 (mtp) REVERT: A 1208 LYS cc_start: 0.7852 (ttpt) cc_final: 0.7266 (pttm) REVERT: A 1211 GLN cc_start: 0.8135 (tp-100) cc_final: 0.7493 (tm-30) outliers start: 25 outliers final: 15 residues processed: 128 average time/residue: 1.1514 time to fit residues: 158.6187 Evaluate side-chains 129 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1243 GLN Chi-restraints excluded: chain A residue 1267 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 GLN A1244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9623 Z= 0.263 Angle : 0.542 9.983 13072 Z= 0.277 Chirality : 0.042 0.194 1513 Planarity : 0.004 0.035 1610 Dihedral : 9.468 88.091 1899 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.94 % Allowed : 15.76 % 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: 1.67 (0.24), residues: 1171 helix: 1.78 (0.18), residues: 796 sheet: 0.55 (0.65), residues: 60 loop : -0.44 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 228 HIS 0.004 0.001 HIS A 141 PHE 0.024 0.002 PHE A 508 TYR 0.030 0.001 TYR A 306 ARG 0.002 0.000 ARG A 908 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 115 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7985 (mtm-85) cc_final: 0.7568 (mtt90) REVERT: A 404 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7800 (mt0) REVERT: A 424 ASN cc_start: 0.7886 (m110) cc_final: 0.7549 (m-40) REVERT: A 802 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.7134 (t70) REVERT: A 848 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8054 (mp) REVERT: A 1159 ASP cc_start: 0.7662 (OUTLIER) cc_final: 0.7271 (t0) REVERT: A 1208 LYS cc_start: 0.7882 (ttpt) cc_final: 0.7342 (mtpp) REVERT: A 1211 GLN cc_start: 0.8204 (tp-100) cc_final: 0.7525 (tm-30) outliers start: 28 outliers final: 17 residues processed: 136 average time/residue: 1.2084 time to fit residues: 176.8700 Evaluate side-chains 133 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1243 GLN Chi-restraints excluded: chain A residue 1267 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 82 optimal weight: 0.2980 chunk 32 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 104 optimal weight: 0.1980 chunk 69 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 9623 Z= 0.143 Angle : 0.494 10.531 13072 Z= 0.251 Chirality : 0.039 0.200 1513 Planarity : 0.003 0.037 1610 Dihedral : 9.101 82.221 1899 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.52 % Allowed : 16.28 % Favored : 81.20 % 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: 1.93 (0.24), residues: 1171 helix: 1.99 (0.18), residues: 797 sheet: 0.50 (0.64), residues: 60 loop : -0.37 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 228 HIS 0.002 0.001 HIS A 141 PHE 0.019 0.001 PHE A 934 TYR 0.028 0.001 TYR A 306 ARG 0.001 0.000 ARG A 783 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7957 (mtm-85) cc_final: 0.7669 (mtt90) REVERT: A 404 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7765 (mt0) REVERT: A 424 ASN cc_start: 0.7858 (m110) cc_final: 0.7518 (m-40) REVERT: A 802 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.7164 (t70) REVERT: A 848 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8030 (mp) REVERT: A 915 MET cc_start: 0.8709 (mtm) cc_final: 0.8422 (mtp) REVERT: A 1159 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7312 (t0) outliers start: 24 outliers final: 17 residues processed: 129 average time/residue: 1.1348 time to fit residues: 157.9461 Evaluate side-chains 132 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1159 ASP Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1267 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 0.9990 chunk 67 optimal weight: 0.4980 chunk 52 optimal weight: 0.4980 chunk 77 optimal weight: 0.8980 chunk 116 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 0.2980 chunk 73 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 9623 Z= 0.151 Angle : 0.498 10.771 13072 Z= 0.252 Chirality : 0.039 0.200 1513 Planarity : 0.003 0.038 1610 Dihedral : 8.917 83.106 1899 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.31 % Allowed : 16.60 % Favored : 81.09 % 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: 1.98 (0.24), residues: 1171 helix: 2.03 (0.18), residues: 797 sheet: 0.47 (0.64), residues: 60 loop : -0.34 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 228 HIS 0.003 0.000 HIS A 141 PHE 0.021 0.001 PHE A 934 TYR 0.027 0.001 TYR A 306 ARG 0.002 0.000 ARG A 144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.7971 (mtm-85) cc_final: 0.7682 (mtt90) REVERT: A 424 ASN cc_start: 0.7884 (m110) cc_final: 0.7525 (m-40) REVERT: A 511 LYS cc_start: 0.7965 (ttpt) cc_final: 0.7717 (mttt) REVERT: A 802 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.7136 (t70) REVERT: A 848 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8051 (mp) REVERT: A 915 MET cc_start: 0.8713 (mtm) cc_final: 0.8440 (mtp) REVERT: A 1208 LYS cc_start: 0.7890 (ttpt) cc_final: 0.7439 (mtpp) outliers start: 22 outliers final: 17 residues processed: 127 average time/residue: 1.1559 time to fit residues: 158.2496 Evaluate side-chains 126 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 953 PHE Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1232 THR Chi-restraints excluded: chain A residue 1267 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 85 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 95 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 HIS ** A 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.177123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.122651 restraints weight = 9649.630| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.81 r_work: 0.3070 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9623 Z= 0.163 Angle : 0.501 10.677 13072 Z= 0.253 Chirality : 0.039 0.201 1513 Planarity : 0.003 0.036 1610 Dihedral : 8.859 84.615 1899 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.21 % Allowed : 16.39 % Favored : 81.41 % 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: 1.98 (0.24), residues: 1171 helix: 2.04 (0.18), residues: 796 sheet: 0.48 (0.65), residues: 60 loop : -0.37 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 228 HIS 0.003 0.001 HIS A 141 PHE 0.023 0.001 PHE A 934 TYR 0.028 0.001 TYR A 306 ARG 0.002 0.000 ARG A 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3537.26 seconds wall clock time: 63 minutes 6.36 seconds (3786.36 seconds total)