Starting phenix.real_space_refine on Thu Mar 14 17:20:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fg2_31574/03_2024/7fg2_31574.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fg2_31574/03_2024/7fg2_31574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fg2_31574/03_2024/7fg2_31574.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fg2_31574/03_2024/7fg2_31574.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fg2_31574/03_2024/7fg2_31574.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fg2_31574/03_2024/7fg2_31574.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 5932 2.51 5 N 1574 2.21 5 O 1795 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 78": "NH1" <-> "NH2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A ARG 682": "NH1" <-> "NH2" Residue "A ARG 685": "NH1" <-> "NH2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 936": "OD1" <-> "OD2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "D ARG 54": "NH1" <-> "NH2" Residue "D TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 105": "OD1" <-> "OD2" 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: 9342 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 8468 Classifications: {'peptide': 1086} Link IDs: {'PTRANS': 50, 'TRANS': 1035} Chain breaks: 2 Chain: "D" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 874 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Time building chain proxies: 5.29, per 1000 atoms: 0.57 Number of scatterers: 9342 At special positions: 0 Unit cell: (92.43, 139.356, 182.016, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 1795 8.00 N 1574 7.00 C 5932 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.01 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.89 Conformation dependent library (CDL) restraints added in 1.8 seconds 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 19 sheets defined 21.6% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 179 through 184 removed outlier: 3.839A pdb=" N GLY A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.704A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.458A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.119A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 756 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 811 through 815 removed outlier: 4.060A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.627A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 883 Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.965A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 941 removed outlier: 4.221A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.766A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 4.245A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1034 Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.605A pdb=" N ASP D 91 " --> pdb=" O LYS D 88 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR D 92 " --> pdb=" O PRO D 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 88 through 92' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.847A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.850A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.561A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 227 removed outlier: 3.981A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 189 Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 379 through 380 removed outlier: 4.682A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 448 through 454 removed outlier: 4.365A pdb=" N ASN A 450 " --> pdb=" O TYR A 495 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TYR A 495 " --> pdb=" O ASN A 450 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU A 452 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLN A 493 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 543 Processing sheet with id=AB2, first strand: chain 'A' and resid 643 through 645 removed outlier: 3.518A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 713 through 722 removed outlier: 6.882A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR A1047 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 725 through 728 Processing sheet with id=AB5, first strand: chain 'A' and resid 735 through 736 removed outlier: 3.548A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1076 through 1077 Processing sheet with id=AB7, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AB8, first strand: chain 'D' and resid 6 through 8 removed outlier: 4.263A pdb=" N CYS D 23 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL D 80 " --> pdb=" O CYS D 23 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 36 through 40 removed outlier: 8.124A pdb=" N TRP D 37 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL D 49 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 93 through 95 278 hydrogen bonds defined for protein. 741 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: 3.11 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3002 1.34 - 1.46: 1876 1.46 - 1.58: 4622 1.58 - 1.69: 0 1.69 - 1.81: 53 Bond restraints: 9553 Sorted by residual: bond pdb=" CA TYR A 612 " pdb=" CB TYR A 612 " ideal model delta sigma weight residual 1.528 1.484 0.043 1.39e-02 5.18e+03 9.79e+00 bond pdb=" C ILE A 726 " pdb=" N LEU A 727 " ideal model delta sigma weight residual 1.331 1.291 0.040 1.36e-02 5.41e+03 8.50e+00 bond pdb=" CB VAL A 687 " pdb=" CG1 VAL A 687 " ideal model delta sigma weight residual 1.521 1.433 0.088 3.30e-02 9.18e+02 7.12e+00 bond pdb=" CA SER A 982 " pdb=" C SER A 982 " ideal model delta sigma weight residual 1.523 1.485 0.038 1.48e-02 4.57e+03 6.70e+00 bond pdb=" CB THR A 299 " pdb=" CG2 THR A 299 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.65e+00 ... (remaining 9548 not shown) Histogram of bond angle deviations from ideal: 99.19 - 106.17: 223 106.17 - 113.15: 5070 113.15 - 120.14: 3378 120.14 - 127.12: 4243 127.12 - 134.10: 78 Bond angle restraints: 12992 Sorted by residual: angle pdb=" N VAL A 483 " pdb=" CA VAL A 483 " pdb=" C VAL A 483 " ideal model delta sigma weight residual 113.71 106.29 7.42 9.50e-01 1.11e+00 6.10e+01 angle pdb=" N SER A 325 " pdb=" CA SER A 325 " pdb=" C SER A 325 " ideal model delta sigma weight residual 107.73 116.63 -8.90 1.34e+00 5.57e-01 4.41e+01 angle pdb=" C LEU A 176 " pdb=" N MET A 177 " pdb=" CA MET A 177 " ideal model delta sigma weight residual 121.54 131.36 -9.82 1.91e+00 2.74e-01 2.65e+01 angle pdb=" C MET A 177 " pdb=" N ASP A 178 " pdb=" CA ASP A 178 " ideal model delta sigma weight residual 121.54 131.32 -9.78 1.91e+00 2.74e-01 2.62e+01 angle pdb=" N SER A 591 " pdb=" CA SER A 591 " pdb=" CB SER A 591 " ideal model delta sigma weight residual 114.17 108.42 5.75 1.14e+00 7.69e-01 2.54e+01 ... (remaining 12987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5144 17.97 - 35.94: 418 35.94 - 53.92: 67 53.92 - 71.89: 17 71.89 - 89.86: 14 Dihedral angle restraints: 5660 sinusoidal: 2182 harmonic: 3478 Sorted by residual: dihedral pdb=" CA ASP A 178 " pdb=" C ASP A 178 " pdb=" N LEU A 179 " pdb=" CA LEU A 179 " ideal model delta harmonic sigma weight residual -180.00 -119.39 -60.61 0 5.00e+00 4.00e-02 1.47e+02 dihedral pdb=" CA SER A 591 " pdb=" C SER A 591 " pdb=" N PHE A 592 " pdb=" CA PHE A 592 " ideal model delta harmonic sigma weight residual 180.00 125.20 54.80 0 5.00e+00 4.00e-02 1.20e+02 dihedral pdb=" CA ALA A 623 " pdb=" C ALA A 623 " pdb=" N ILE A 624 " pdb=" CA ILE A 624 " ideal model delta harmonic sigma weight residual 180.00 -125.21 -54.79 0 5.00e+00 4.00e-02 1.20e+02 ... (remaining 5657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 959 0.043 - 0.086: 340 0.086 - 0.129: 132 0.129 - 0.173: 26 0.173 - 0.216: 8 Chirality restraints: 1465 Sorted by residual: chirality pdb=" CB THR A 274 " pdb=" CA THR A 274 " pdb=" OG1 THR A 274 " pdb=" CG2 THR A 274 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB THR A 827 " pdb=" CA THR A 827 " pdb=" OG1 THR A 827 " pdb=" CG2 THR A 827 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA VAL A 705 " pdb=" N VAL A 705 " pdb=" C VAL A 705 " pdb=" CB VAL A 705 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1462 not shown) Planarity restraints: 1689 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 599 " -0.050 5.00e-02 4.00e+02 7.71e-02 9.51e+00 pdb=" N PRO A 600 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 600 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 600 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 714 " 0.051 5.00e-02 4.00e+02 7.67e-02 9.41e+00 pdb=" N PRO A 715 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 715 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 715 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 321 " -0.042 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO A 322 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " -0.035 5.00e-02 4.00e+02 ... (remaining 1686 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 253 2.62 - 3.19: 9728 3.19 - 3.76: 14685 3.76 - 4.33: 20347 4.33 - 4.90: 31549 Nonbonded interactions: 76562 Sorted by model distance: nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.053 2.440 nonbonded pdb=" O GLU A 661 " pdb=" OH TYR A 695 " model vdw 2.058 2.440 nonbonded pdb=" OD1 ASN A 709 " pdb=" N ASN A 710 " model vdw 2.058 2.520 nonbonded pdb=" OG1 THR A 478 " pdb=" OD1 ASN A 481 " model vdw 2.061 2.440 nonbonded pdb=" OG SER D 18 " pdb=" OD1 ASN D 85 " model vdw 2.091 2.440 ... (remaining 76557 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 group one per residue 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: 0.790 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: 4.170 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 28.730 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 9553 Z= 0.451 Angle : 1.134 9.825 12992 Z= 0.679 Chirality : 0.053 0.216 1465 Planarity : 0.006 0.077 1689 Dihedral : 14.434 89.862 3405 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 32.64 Ramachandran Plot: Outliers : 0.42 % Allowed : 17.84 % Favored : 81.74 % Rotamer: Outliers : 0.19 % Allowed : 0.19 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.70 % 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: -3.95 (0.22), residues: 1194 helix: -0.70 (0.34), residues: 222 sheet: -2.12 (0.34), residues: 217 loop : -3.63 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A1102 HIS 0.006 0.002 HIS A1083 PHE 0.028 0.003 PHE A 797 TYR 0.027 0.003 TYR A 789 ARG 0.011 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 222 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 SER cc_start: 0.7650 (t) cc_final: 0.7359 (t) REVERT: A 137 ASN cc_start: 0.6800 (p0) cc_final: 0.6326 (p0) REVERT: A 220 PHE cc_start: 0.7007 (t80) cc_final: 0.6699 (t80) REVERT: A 223 LEU cc_start: 0.8221 (mp) cc_final: 0.8004 (mp) REVERT: A 350 VAL cc_start: 0.8770 (p) cc_final: 0.8000 (p) REVERT: A 400 PHE cc_start: 0.8231 (p90) cc_final: 0.7715 (p90) REVERT: A 559 PHE cc_start: 0.7741 (m-10) cc_final: 0.7463 (m-10) REVERT: A 738 CYS cc_start: 0.9078 (t) cc_final: 0.8693 (t) REVERT: A 818 ILE cc_start: 0.7786 (mt) cc_final: 0.6824 (mt) REVERT: A 823 PHE cc_start: 0.7910 (t80) cc_final: 0.7635 (t80) REVERT: A 900 MET cc_start: 0.7036 (mpp) cc_final: 0.6520 (mpp) REVERT: A 1010 GLN cc_start: 0.8808 (tp-100) cc_final: 0.8271 (tp-100) REVERT: D 71 ILE cc_start: 0.3741 (tp) cc_final: 0.3287 (tp) REVERT: D 84 MET cc_start: 0.5086 (pmm) cc_final: 0.4704 (pmm) outliers start: 2 outliers final: 0 residues processed: 222 average time/residue: 0.2065 time to fit residues: 63.8431 Evaluate side-chains 167 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 30.0000 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 81 ASN A 211 ASN A 448 ASN A 606 ASN A 824 ASN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN A 935 GLN A1005 GLN A1054 GLN ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9553 Z= 0.260 Angle : 0.778 10.077 12992 Z= 0.420 Chirality : 0.049 0.245 1465 Planarity : 0.006 0.069 1689 Dihedral : 7.587 59.477 1296 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 22.55 Ramachandran Plot: Outliers : 0.42 % Allowed : 15.49 % Favored : 84.09 % Rotamer: Outliers : 0.39 % Allowed : 5.31 % Favored : 94.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.61 % 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: -3.48 (0.23), residues: 1194 helix: -0.03 (0.34), residues: 226 sheet: -1.91 (0.35), residues: 204 loop : -3.39 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.007 0.001 HIS A 655 PHE 0.025 0.002 PHE A1121 TYR 0.019 0.002 TYR A 451 ARG 0.012 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 219 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8148 (t) cc_final: 0.7900 (m) REVERT: A 52 GLN cc_start: 0.8308 (pp30) cc_final: 0.7624 (pp30) REVERT: A 137 ASN cc_start: 0.6404 (p0) cc_final: 0.5806 (p0) REVERT: A 318 PHE cc_start: 0.6667 (m-80) cc_final: 0.6402 (m-80) REVERT: A 350 VAL cc_start: 0.8461 (p) cc_final: 0.7478 (p) REVERT: A 400 PHE cc_start: 0.8236 (p90) cc_final: 0.7722 (p90) REVERT: A 619 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6651 (mm-30) REVERT: A 729 VAL cc_start: 0.8160 (t) cc_final: 0.7825 (p) REVERT: A 773 GLU cc_start: 0.6982 (tm-30) cc_final: 0.6549 (tm-30) REVERT: A 774 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7720 (mm-40) REVERT: A 777 ASN cc_start: 0.8125 (m-40) cc_final: 0.7778 (m-40) REVERT: A 900 MET cc_start: 0.7039 (mpp) cc_final: 0.6327 (mpp) REVERT: A 933 LYS cc_start: 0.8551 (tttm) cc_final: 0.8063 (tttt) REVERT: A 985 ASP cc_start: 0.7846 (m-30) cc_final: 0.7645 (m-30) REVERT: A 1005 GLN cc_start: 0.9031 (tp40) cc_final: 0.8571 (tp40) REVERT: A 1010 GLN cc_start: 0.8652 (tp-100) cc_final: 0.8226 (tp-100) REVERT: A 1012 LEU cc_start: 0.8425 (mt) cc_final: 0.8160 (mp) REVERT: A 1028 LYS cc_start: 0.6065 (tptt) cc_final: 0.5833 (tptt) REVERT: D 71 ILE cc_start: 0.3394 (tp) cc_final: 0.3049 (tp) REVERT: D 84 MET cc_start: 0.4977 (pmm) cc_final: 0.4309 (pmm) outliers start: 4 outliers final: 0 residues processed: 220 average time/residue: 0.1977 time to fit residues: 60.7809 Evaluate side-chains 177 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 8.9990 chunk 33 optimal weight: 20.0000 chunk 89 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 606 ASN A 625 HIS ** A 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN D 83 GLN ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9553 Z= 0.198 Angle : 0.701 9.626 12992 Z= 0.377 Chirality : 0.046 0.175 1465 Planarity : 0.005 0.061 1689 Dihedral : 6.993 59.870 1296 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.42 % Allowed : 14.74 % Favored : 84.84 % Rotamer: Outliers : 0.29 % Allowed : 5.21 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.44 % 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: -3.20 (0.23), residues: 1194 helix: 0.44 (0.35), residues: 229 sheet: -1.63 (0.36), residues: 198 loop : -3.32 (0.20), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.005 0.001 HIS A 655 PHE 0.023 0.002 PHE A 592 TYR 0.014 0.001 TYR A 421 ARG 0.007 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 225 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8192 (pp30) cc_final: 0.7852 (pp30) REVERT: A 220 PHE cc_start: 0.7210 (t80) cc_final: 0.6618 (t80) REVERT: A 274 THR cc_start: 0.7597 (t) cc_final: 0.7303 (t) REVERT: A 303 LEU cc_start: 0.8449 (tt) cc_final: 0.8206 (tt) REVERT: A 350 VAL cc_start: 0.8493 (p) cc_final: 0.7431 (p) REVERT: A 400 PHE cc_start: 0.8074 (p90) cc_final: 0.7531 (p90) REVERT: A 613 GLN cc_start: 0.8013 (mt0) cc_final: 0.7305 (pt0) REVERT: A 729 VAL cc_start: 0.8144 (t) cc_final: 0.7919 (p) REVERT: A 732 THR cc_start: 0.8577 (p) cc_final: 0.8339 (p) REVERT: A 738 CYS cc_start: 0.8543 (t) cc_final: 0.8305 (t) REVERT: A 858 LEU cc_start: 0.8732 (mt) cc_final: 0.8530 (mt) REVERT: A 900 MET cc_start: 0.7028 (mpp) cc_final: 0.6689 (mpp) REVERT: A 985 ASP cc_start: 0.8079 (m-30) cc_final: 0.7765 (m-30) REVERT: A 1005 GLN cc_start: 0.8975 (tp40) cc_final: 0.8515 (tp40) REVERT: A 1010 GLN cc_start: 0.8663 (tp-100) cc_final: 0.8296 (tp40) REVERT: A 1012 LEU cc_start: 0.8517 (mt) cc_final: 0.8188 (mp) REVERT: A 1031 GLU cc_start: 0.7416 (mt-10) cc_final: 0.6639 (mt-10) REVERT: A 1043 CYS cc_start: 0.3334 (m) cc_final: 0.3116 (m) REVERT: A 1052 PHE cc_start: 0.7893 (m-10) cc_final: 0.7634 (m-10) REVERT: D 85 ASN cc_start: 0.6646 (m-40) cc_final: 0.6244 (p0) outliers start: 3 outliers final: 0 residues processed: 225 average time/residue: 0.1994 time to fit residues: 62.7247 Evaluate side-chains 176 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.0470 chunk 81 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 11 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 overall best weight: 1.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9553 Z= 0.242 Angle : 0.714 9.799 12992 Z= 0.383 Chirality : 0.048 0.181 1465 Planarity : 0.005 0.072 1689 Dihedral : 6.947 60.440 1296 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.42 % Allowed : 15.08 % Favored : 84.51 % Rotamer: Outliers : 0.10 % Allowed : 4.92 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.35 % 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: -3.19 (0.23), residues: 1194 helix: 0.46 (0.35), residues: 222 sheet: -1.87 (0.35), residues: 200 loop : -3.20 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 107 HIS 0.004 0.001 HIS A 655 PHE 0.027 0.002 PHE A1121 TYR 0.016 0.002 TYR A 453 ARG 0.008 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.7977 (t) cc_final: 0.7683 (m) REVERT: A 52 GLN cc_start: 0.8198 (pp30) cc_final: 0.7714 (pp30) REVERT: A 220 PHE cc_start: 0.7498 (t80) cc_final: 0.7218 (t80) REVERT: A 221 SER cc_start: 0.7573 (m) cc_final: 0.7330 (m) REVERT: A 274 THR cc_start: 0.7075 (t) cc_final: 0.6867 (t) REVERT: A 350 VAL cc_start: 0.8504 (p) cc_final: 0.7488 (p) REVERT: A 374 PHE cc_start: 0.5341 (p90) cc_final: 0.5027 (p90) REVERT: A 400 PHE cc_start: 0.7993 (p90) cc_final: 0.7507 (p90) REVERT: A 608 VAL cc_start: 0.6494 (p) cc_final: 0.6056 (p) REVERT: A 613 GLN cc_start: 0.8049 (mt0) cc_final: 0.7288 (pt0) REVERT: A 627 ASP cc_start: 0.7316 (p0) cc_final: 0.6803 (p0) REVERT: A 697 MET cc_start: 0.6904 (tmm) cc_final: 0.6567 (tmm) REVERT: A 729 VAL cc_start: 0.8177 (t) cc_final: 0.7931 (p) REVERT: A 900 MET cc_start: 0.6868 (mpp) cc_final: 0.6587 (mpp) REVERT: A 985 ASP cc_start: 0.8136 (m-30) cc_final: 0.7769 (m-30) REVERT: A 1005 GLN cc_start: 0.9052 (tp40) cc_final: 0.8578 (tp40) REVERT: A 1010 GLN cc_start: 0.8688 (tp-100) cc_final: 0.8114 (tp40) REVERT: A 1039 ARG cc_start: 0.6955 (ptp90) cc_final: 0.6579 (ptp90) REVERT: A 1063 LEU cc_start: 0.7529 (mp) cc_final: 0.7182 (mp) REVERT: D 33 TYR cc_start: 0.6434 (m-80) cc_final: 0.6203 (m-80) REVERT: D 85 ASN cc_start: 0.7362 (m-40) cc_final: 0.6254 (p0) outliers start: 1 outliers final: 0 residues processed: 211 average time/residue: 0.2008 time to fit residues: 59.8170 Evaluate side-chains 173 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 0.0070 chunk 1 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 98 optimal weight: 0.0470 chunk 79 optimal weight: 0.0030 chunk 0 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 overall best weight: 0.3506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1088 HIS ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9553 Z= 0.181 Angle : 0.673 10.788 12992 Z= 0.359 Chirality : 0.045 0.163 1465 Planarity : 0.005 0.052 1689 Dihedral : 6.476 57.156 1296 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.48 % Favored : 87.10 % Rotamer: Outliers : 0.10 % Allowed : 2.80 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.35 % 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: -2.96 (0.23), residues: 1194 helix: 0.86 (0.36), residues: 210 sheet: -1.61 (0.36), residues: 202 loop : -3.11 (0.20), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.004 0.001 HIS A 655 PHE 0.022 0.001 PHE A1121 TYR 0.015 0.001 TYR D 98 ARG 0.004 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 225 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7861 (pp30) cc_final: 0.7332 (pp30) REVERT: A 221 SER cc_start: 0.7718 (m) cc_final: 0.7510 (m) REVERT: A 350 VAL cc_start: 0.8519 (p) cc_final: 0.7354 (p) REVERT: A 374 PHE cc_start: 0.5119 (p90) cc_final: 0.4912 (p90) REVERT: A 400 PHE cc_start: 0.7865 (p90) cc_final: 0.7213 (p90) REVERT: A 613 GLN cc_start: 0.7931 (mt0) cc_final: 0.7243 (pt0) REVERT: A 627 ASP cc_start: 0.7050 (p0) cc_final: 0.6543 (p0) REVERT: A 727 LEU cc_start: 0.8280 (mp) cc_final: 0.8061 (mp) REVERT: A 802 PHE cc_start: 0.7065 (m-80) cc_final: 0.6771 (m-80) REVERT: A 858 LEU cc_start: 0.8744 (mt) cc_final: 0.8210 (mt) REVERT: A 859 THR cc_start: 0.8321 (t) cc_final: 0.8040 (m) REVERT: A 900 MET cc_start: 0.6837 (mpp) cc_final: 0.6627 (mpp) REVERT: A 985 ASP cc_start: 0.8065 (m-30) cc_final: 0.7727 (m-30) REVERT: A 1002 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8307 (tm-30) REVERT: A 1005 GLN cc_start: 0.9026 (tp40) cc_final: 0.8466 (tp40) REVERT: A 1028 LYS cc_start: 0.6601 (tptp) cc_final: 0.5857 (tppp) REVERT: A 1039 ARG cc_start: 0.6736 (ptp90) cc_final: 0.6431 (ptp90) REVERT: A 1075 PHE cc_start: 0.6292 (m-10) cc_final: 0.6063 (m-10) REVERT: D 85 ASN cc_start: 0.7362 (m-40) cc_final: 0.6260 (p0) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.1938 time to fit residues: 61.0771 Evaluate side-chains 176 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 67 optimal weight: 0.0270 chunk 28 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 60 optimal weight: 0.0970 chunk 111 optimal weight: 5.9990 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9553 Z= 0.175 Angle : 0.649 10.277 12992 Z= 0.345 Chirality : 0.045 0.162 1465 Planarity : 0.005 0.051 1689 Dihedral : 6.276 57.073 1296 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.40 % Favored : 87.19 % Rotamer: Outliers : 0.10 % Allowed : 2.12 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.35 % 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: -2.84 (0.23), residues: 1194 helix: 0.88 (0.36), residues: 210 sheet: -1.45 (0.37), residues: 202 loop : -3.02 (0.20), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 107 HIS 0.002 0.001 HIS A 655 PHE 0.022 0.001 PHE A1075 TYR 0.018 0.001 TYR A1110 ARG 0.008 0.001 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 212 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7856 (pp30) cc_final: 0.7360 (pp30) REVERT: A 220 PHE cc_start: 0.7226 (t80) cc_final: 0.6840 (t80) REVERT: A 248 TYR cc_start: 0.6144 (t80) cc_final: 0.4761 (m-80) REVERT: A 291 CYS cc_start: 0.7526 (p) cc_final: 0.7308 (m) REVERT: A 350 VAL cc_start: 0.8416 (p) cc_final: 0.7277 (p) REVERT: A 400 PHE cc_start: 0.7805 (p90) cc_final: 0.7179 (p90) REVERT: A 613 GLN cc_start: 0.7807 (mt0) cc_final: 0.7106 (pt0) REVERT: A 627 ASP cc_start: 0.7270 (p0) cc_final: 0.6694 (p0) REVERT: A 702 GLU cc_start: 0.7129 (tm-30) cc_final: 0.6710 (tm-30) REVERT: A 747 THR cc_start: 0.7384 (m) cc_final: 0.6983 (p) REVERT: A 802 PHE cc_start: 0.6935 (m-80) cc_final: 0.6687 (m-80) REVERT: A 858 LEU cc_start: 0.8721 (mt) cc_final: 0.8459 (mt) REVERT: A 900 MET cc_start: 0.6859 (mpp) cc_final: 0.6655 (mpp) REVERT: A 985 ASP cc_start: 0.8086 (m-30) cc_final: 0.7636 (m-30) REVERT: A 1002 GLN cc_start: 0.8728 (tm-30) cc_final: 0.8266 (tm-30) REVERT: A 1005 GLN cc_start: 0.9007 (tp40) cc_final: 0.8440 (tp40) REVERT: A 1028 LYS cc_start: 0.6720 (tptp) cc_final: 0.5993 (ttmt) REVERT: A 1039 ARG cc_start: 0.6595 (ptp90) cc_final: 0.6216 (ptp90) REVERT: A 1075 PHE cc_start: 0.6689 (m-10) cc_final: 0.6187 (m-10) REVERT: D 35 MET cc_start: -0.0266 (ptt) cc_final: -0.0618 (ptt) REVERT: D 85 ASN cc_start: 0.7440 (m-40) cc_final: 0.6409 (p0) outliers start: 1 outliers final: 0 residues processed: 212 average time/residue: 0.2076 time to fit residues: 61.2403 Evaluate side-chains 170 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 954 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9553 Z= 0.249 Angle : 0.706 9.289 12992 Z= 0.376 Chirality : 0.047 0.173 1465 Planarity : 0.005 0.055 1689 Dihedral : 6.520 57.667 1296 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.34 % Allowed : 14.32 % Favored : 85.34 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.35 % 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: -2.99 (0.23), residues: 1194 helix: 0.59 (0.35), residues: 218 sheet: -1.56 (0.36), residues: 202 loop : -3.11 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 107 HIS 0.006 0.001 HIS A1064 PHE 0.027 0.002 PHE A1075 TYR 0.020 0.002 TYR A 756 ARG 0.006 0.001 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8137 (t) cc_final: 0.7829 (m) REVERT: A 52 GLN cc_start: 0.8014 (pp30) cc_final: 0.7518 (pp30) REVERT: A 220 PHE cc_start: 0.7624 (t80) cc_final: 0.7334 (t80) REVERT: A 248 TYR cc_start: 0.6531 (t80) cc_final: 0.5141 (m-80) REVERT: A 274 THR cc_start: 0.7263 (t) cc_final: 0.7056 (t) REVERT: A 350 VAL cc_start: 0.8490 (p) cc_final: 0.7396 (p) REVERT: A 400 PHE cc_start: 0.7794 (p90) cc_final: 0.7431 (p90) REVERT: A 613 GLN cc_start: 0.8023 (mt0) cc_final: 0.7245 (pt0) REVERT: A 627 ASP cc_start: 0.7616 (p0) cc_final: 0.7105 (p0) REVERT: A 747 THR cc_start: 0.7657 (m) cc_final: 0.7206 (p) REVERT: A 858 LEU cc_start: 0.8736 (mt) cc_final: 0.8413 (mt) REVERT: A 859 THR cc_start: 0.8443 (t) cc_final: 0.8169 (p) REVERT: A 985 ASP cc_start: 0.8064 (m-30) cc_final: 0.7675 (m-30) REVERT: D 85 ASN cc_start: 0.7169 (m-40) cc_final: 0.6035 (p0) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.2018 time to fit residues: 56.8532 Evaluate side-chains 159 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 72 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 109 optimal weight: 0.0170 chunk 100 optimal weight: 0.0570 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 926 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9553 Z= 0.183 Angle : 0.653 8.704 12992 Z= 0.346 Chirality : 0.045 0.164 1465 Planarity : 0.004 0.043 1689 Dihedral : 6.178 55.041 1296 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.34 % Allowed : 12.81 % Favored : 86.85 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -2.75 (0.24), residues: 1194 helix: 0.84 (0.35), residues: 210 sheet: -1.36 (0.37), residues: 211 loop : -2.94 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 37 HIS 0.003 0.001 HIS A 655 PHE 0.018 0.001 PHE A1121 TYR 0.015 0.001 TYR A 453 ARG 0.007 0.001 ARG D 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8043 (pp30) cc_final: 0.7620 (pp30) REVERT: A 220 PHE cc_start: 0.7425 (t80) cc_final: 0.7223 (t80) REVERT: A 248 TYR cc_start: 0.6222 (t80) cc_final: 0.4775 (m-80) REVERT: A 350 VAL cc_start: 0.8401 (p) cc_final: 0.7183 (p) REVERT: A 374 PHE cc_start: 0.5498 (p90) cc_final: 0.5123 (p90) REVERT: A 400 PHE cc_start: 0.7647 (p90) cc_final: 0.7034 (p90) REVERT: A 613 GLN cc_start: 0.8029 (mt0) cc_final: 0.7274 (pt0) REVERT: A 627 ASP cc_start: 0.7410 (p0) cc_final: 0.6949 (p0) REVERT: A 747 THR cc_start: 0.7497 (m) cc_final: 0.7149 (p) REVERT: A 858 LEU cc_start: 0.8699 (mt) cc_final: 0.8322 (mt) REVERT: A 859 THR cc_start: 0.8263 (t) cc_final: 0.8047 (p) REVERT: A 867 ASP cc_start: 0.7510 (m-30) cc_final: 0.7217 (m-30) REVERT: A 985 ASP cc_start: 0.8070 (m-30) cc_final: 0.7627 (m-30) REVERT: A 1002 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8405 (tm-30) REVERT: A 1005 GLN cc_start: 0.8989 (tp40) cc_final: 0.8435 (tp40) REVERT: A 1028 LYS cc_start: 0.6609 (tptp) cc_final: 0.5936 (ttpt) REVERT: D 85 ASN cc_start: 0.7157 (m-40) cc_final: 0.6043 (p0) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2028 time to fit residues: 59.0290 Evaluate side-chains 165 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 83 optimal weight: 0.5980 chunk 32 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 ASN A1054 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9553 Z= 0.257 Angle : 0.710 7.627 12992 Z= 0.376 Chirality : 0.048 0.351 1465 Planarity : 0.005 0.042 1689 Dihedral : 6.401 54.983 1296 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.34 % Allowed : 14.41 % Favored : 85.26 % Rotamer: Outliers : 0.10 % Allowed : 0.48 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -2.92 (0.23), residues: 1194 helix: 0.53 (0.34), residues: 218 sheet: -1.60 (0.35), residues: 216 loop : -2.99 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 107 HIS 0.004 0.001 HIS A1064 PHE 0.032 0.002 PHE A1121 TYR 0.019 0.002 TYR D 98 ARG 0.004 0.001 ARG A 634 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8125 (t) cc_final: 0.7813 (m) REVERT: A 52 GLN cc_start: 0.8253 (pp30) cc_final: 0.7776 (pp30) REVERT: A 118 LEU cc_start: 0.7763 (tp) cc_final: 0.7523 (tp) REVERT: A 177 MET cc_start: 0.4355 (ppp) cc_final: 0.3322 (mpp) REVERT: A 289 VAL cc_start: 0.8771 (p) cc_final: 0.8445 (p) REVERT: A 350 VAL cc_start: 0.8513 (p) cc_final: 0.7353 (p) REVERT: A 400 PHE cc_start: 0.7728 (p90) cc_final: 0.7133 (p90) REVERT: A 613 GLN cc_start: 0.8130 (mt0) cc_final: 0.7658 (pt0) REVERT: A 627 ASP cc_start: 0.7609 (p0) cc_final: 0.7092 (p0) REVERT: A 658 ASN cc_start: 0.8036 (OUTLIER) cc_final: 0.7380 (t0) REVERT: A 660 TYR cc_start: 0.7516 (m-10) cc_final: 0.7144 (m-10) REVERT: A 732 THR cc_start: 0.8737 (p) cc_final: 0.8519 (p) REVERT: A 747 THR cc_start: 0.7617 (m) cc_final: 0.7205 (p) REVERT: A 858 LEU cc_start: 0.8859 (mt) cc_final: 0.8443 (mt) REVERT: A 859 THR cc_start: 0.8379 (t) cc_final: 0.8165 (p) REVERT: A 900 MET cc_start: 0.6690 (mpp) cc_final: 0.6335 (mpp) REVERT: A 985 ASP cc_start: 0.7796 (m-30) cc_final: 0.7534 (m-30) REVERT: A 1005 GLN cc_start: 0.9063 (tp40) cc_final: 0.8520 (tp-100) REVERT: D 85 ASN cc_start: 0.7203 (m-40) cc_final: 0.6006 (p0) outliers start: 1 outliers final: 0 residues processed: 199 average time/residue: 0.2029 time to fit residues: 57.7254 Evaluate side-chains 166 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 109 optimal weight: 0.0770 chunk 94 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 28 optimal weight: 0.3980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 ASN A 954 GLN A1010 GLN A1054 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6359 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9553 Z= 0.175 Angle : 0.660 7.702 12992 Z= 0.349 Chirality : 0.046 0.186 1465 Planarity : 0.004 0.042 1689 Dihedral : 6.105 49.188 1296 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.90 % Favored : 86.85 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -2.76 (0.23), residues: 1194 helix: 0.70 (0.36), residues: 210 sheet: -1.38 (0.37), residues: 201 loop : -2.89 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 107 HIS 0.002 0.001 HIS A 655 PHE 0.022 0.001 PHE A 55 TYR 0.015 0.001 TYR D 98 ARG 0.005 0.000 ARG A1107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8016 (t) cc_final: 0.7711 (m) REVERT: A 52 GLN cc_start: 0.8093 (pp30) cc_final: 0.7668 (pp30) REVERT: A 177 MET cc_start: 0.3911 (ppp) cc_final: 0.3402 (mpp) REVERT: A 305 SER cc_start: 0.8295 (p) cc_final: 0.8008 (p) REVERT: A 350 VAL cc_start: 0.8407 (p) cc_final: 0.7171 (p) REVERT: A 374 PHE cc_start: 0.5779 (p90) cc_final: 0.5468 (p90) REVERT: A 400 PHE cc_start: 0.7584 (p90) cc_final: 0.7103 (p90) REVERT: A 613 GLN cc_start: 0.8086 (mt0) cc_final: 0.7671 (pt0) REVERT: A 627 ASP cc_start: 0.7466 (p0) cc_final: 0.6938 (p0) REVERT: A 747 THR cc_start: 0.7543 (m) cc_final: 0.7225 (p) REVERT: A 858 LEU cc_start: 0.8713 (mt) cc_final: 0.8331 (mt) REVERT: A 859 THR cc_start: 0.8289 (t) cc_final: 0.8050 (p) REVERT: A 985 ASP cc_start: 0.7809 (m-30) cc_final: 0.7535 (m-30) REVERT: A 1002 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8418 (tm-30) REVERT: A 1005 GLN cc_start: 0.8984 (tp40) cc_final: 0.8420 (tp40) REVERT: A 1028 LYS cc_start: 0.6807 (tptp) cc_final: 0.5983 (ttpt) REVERT: A 1075 PHE cc_start: 0.5789 (m-10) cc_final: 0.5503 (m-10) REVERT: D 85 ASN cc_start: 0.7127 (m-40) cc_final: 0.5950 (p0) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.1874 time to fit residues: 53.9498 Evaluate side-chains 171 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 39 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 11 optimal weight: 0.0170 chunk 17 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.183196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.153343 restraints weight = 26750.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.155979 restraints weight = 16922.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.157861 restraints weight = 12016.304| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9553 Z= 0.187 Angle : 0.661 7.655 12992 Z= 0.349 Chirality : 0.045 0.158 1465 Planarity : 0.004 0.043 1689 Dihedral : 6.067 48.403 1296 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.98 % Favored : 86.77 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -2.70 (0.23), residues: 1194 helix: 0.70 (0.36), residues: 210 sheet: -1.25 (0.36), residues: 219 loop : -2.89 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 37 HIS 0.005 0.001 HIS A1083 PHE 0.023 0.001 PHE A1121 TYR 0.013 0.001 TYR A 453 ARG 0.005 0.000 ARG A1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2110.02 seconds wall clock time: 38 minutes 48.87 seconds (2328.87 seconds total)