Starting phenix.real_space_refine (version: dev) on Mon Dec 12 06:28:52 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fg2_31574/12_2022/7fg2_31574.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fg2_31574/12_2022/7fg2_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_31574/12_2022/7fg2_31574.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fg2_31574/12_2022/7fg2_31574.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fg2_31574/12_2022/7fg2_31574.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fg2_31574/12_2022/7fg2_31574.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4807/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: 5.36, 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: 3.45 Conformation dependent library (CDL) restraints added in 1.5 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: 0.59 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: 3.30 Time building geometry restraints manager: 3.82 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 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. 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.760 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.070 Process input model: 27.580 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 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 : 32.69 Ramachandran Plot: Outliers : 0.42 % Allowed : 17.84 % Favored : 81.74 % Rotamer Outliers : 0.19 % 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 *********************** 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 : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 222 average time/residue: 0.2066 time to fit residues: 64.5656 Evaluate side-chains 163 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.095 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5144 ------------------------------------------------------------------------------- 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: 0.6980 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: 2.9990 chunk 108 optimal weight: 30.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 777 ASN A 824 ASN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN A 928 ASN A 935 GLN A1005 GLN A1010 GLN A1054 GLN ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 9553 Z= 0.264 Angle : 0.776 10.356 12992 Z= 0.418 Chirality : 0.049 0.225 1465 Planarity : 0.006 0.068 1689 Dihedral : 7.559 59.039 1296 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 22.50 Ramachandran Plot: Outliers : 0.42 % Allowed : 16.00 % Favored : 83.58 % Rotamer Outliers : 0.48 % 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: -3.49 (0.23), residues: 1194 helix: -0.03 (0.34), residues: 227 sheet: -1.89 (0.35), residues: 204 loop : -3.40 (0.20), residues: 763 *********************** 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 221 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 216 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 218 average time/residue: 0.1957 time to fit residues: 60.3293 Evaluate side-chains 172 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 1.010 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0718 time to fit residues: 1.4127 ------------------------------------------------------------------------------- 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: 0.6980 chunk 29 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 chunk 116 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 107 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 777 ASN ** A 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.6332 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 9553 Z= 0.194 Angle : 0.705 9.695 12992 Z= 0.379 Chirality : 0.046 0.214 1465 Planarity : 0.005 0.060 1689 Dihedral : 6.921 59.675 1296 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.42 % Allowed : 13.65 % Favored : 85.93 % Rotamer Outliers : 0.29 % 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: -3.22 (0.23), residues: 1194 helix: 0.43 (0.35), residues: 229 sheet: -1.68 (0.35), residues: 210 loop : -3.34 (0.20), residues: 755 *********************** 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 227 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 224 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 224 average time/residue: 0.2026 time to fit residues: 63.7508 Evaluate side-chains 172 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.117 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5078 ------------------------------------------------------------------------------- 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: 9.9990 chunk 81 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 115 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 HIS ** A 901 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: 0.6348 moved from start: 0.3282 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= 0.204 Angle : 0.681 9.881 12992 Z= 0.366 Chirality : 0.046 0.186 1465 Planarity : 0.005 0.057 1689 Dihedral : 6.733 60.149 1296 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.42 % Allowed : 14.49 % Favored : 85.09 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.26 % 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: -3.04 (0.23), residues: 1194 helix: 0.59 (0.36), residues: 226 sheet: -1.65 (0.34), residues: 208 loop : -3.17 (0.20), residues: 760 *********************** 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 214 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 213 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 213 average time/residue: 0.1961 time to fit residues: 59.6131 Evaluate side-chains 166 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.084 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4752 ------------------------------------------------------------------------------- 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: 0.6980 chunk 1 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 29 optimal weight: 0.2980 chunk 38 optimal weight: 5.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 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: 0.6289 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 9553 Z= 0.188 Angle : 0.664 9.775 12992 Z= 0.354 Chirality : 0.046 0.177 1465 Planarity : 0.004 0.053 1689 Dihedral : 6.422 59.027 1296 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.50 % Allowed : 13.15 % Favored : 86.35 % Rotamer Outliers : 0.19 % 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: -2.80 (0.24), residues: 1194 helix: 0.94 (0.36), residues: 212 sheet: -1.39 (0.35), residues: 220 loop : -3.06 (0.21), residues: 762 *********************** 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 213 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 211 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 212 average time/residue: 0.1956 time to fit residues: 59.3301 Evaluate side-chains 159 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.104 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4909 ------------------------------------------------------------------------------- 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: 6.9990 chunk 22 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 9 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS ** 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: 0.6458 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.083 9553 Z= 0.344 Angle : 0.801 10.661 12992 Z= 0.423 Chirality : 0.049 0.187 1465 Planarity : 0.005 0.060 1689 Dihedral : 7.038 57.371 1296 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 24.78 Ramachandran Plot: Outliers : 0.50 % Allowed : 15.33 % Favored : 84.17 % Rotamer Outliers : 0.19 % 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: -3.17 (0.23), residues: 1194 helix: 0.26 (0.33), residues: 223 sheet: -1.73 (0.35), residues: 204 loop : -3.17 (0.20), residues: 767 *********************** 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 192 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 190 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 191 average time/residue: 0.1981 time to fit residues: 54.5730 Evaluate side-chains 157 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 1.022 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1138 time to fit residues: 1.6072 ------------------------------------------------------------------------------- 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: 4.9990 chunk 65 optimal weight: 0.0000 chunk 84 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 45 optimal weight: 20.0000 overall best weight: 1.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6393 moved from start: 0.4045 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 : 0.723 8.765 12992 Z= 0.384 Chirality : 0.047 0.193 1465 Planarity : 0.005 0.083 1689 Dihedral : 6.757 52.199 1296 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.42 % Allowed : 13.32 % Favored : 86.26 % Rotamer Outliers : 0.00 % 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: -3.04 (0.23), residues: 1194 helix: 0.32 (0.34), residues: 223 sheet: -1.48 (0.35), residues: 218 loop : -3.14 (0.21), residues: 753 *********************** 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 205 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.1990 time to fit residues: 58.7862 Evaluate side-chains 165 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.111 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4427 ------------------------------------------------------------------------------- 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: 0.8980 chunk 22 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 78 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** A1088 HIS ** 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: 0.6313 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 9553 Z= 0.183 Angle : 0.673 8.250 12992 Z= 0.358 Chirality : 0.045 0.162 1465 Planarity : 0.005 0.044 1689 Dihedral : 6.282 51.538 1296 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.81 % Favored : 86.77 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.87 (0.23), residues: 1194 helix: 0.52 (0.35), residues: 220 sheet: -1.46 (0.35), residues: 221 loop : -3.00 (0.21), residues: 753 *********************** 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 198 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2084 time to fit residues: 58.8112 Evaluate side-chains 161 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 0.972 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4546 ------------------------------------------------------------------------------- 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: 0.9990 chunk 109 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 46 optimal weight: 0.4980 chunk 83 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6333 moved from start: 0.4701 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= 0.208 Angle : 0.694 7.673 12992 Z= 0.367 Chirality : 0.046 0.162 1465 Planarity : 0.005 0.044 1689 Dihedral : 6.334 50.572 1296 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.34 % Allowed : 13.07 % Favored : 86.60 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.83 (0.23), residues: 1194 helix: 0.38 (0.34), residues: 226 sheet: -1.31 (0.35), residues: 231 loop : -3.00 (0.21), residues: 737 *********************** 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 187 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2224 time to fit residues: 58.9963 Evaluate side-chains 160 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.108 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5835 ------------------------------------------------------------------------------- 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: 6.9990 chunk 78 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 9553 Z= 0.218 Angle : 0.714 11.794 12992 Z= 0.374 Chirality : 0.046 0.163 1465 Planarity : 0.005 0.044 1689 Dihedral : 6.292 49.715 1296 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.34 % Allowed : 13.65 % Favored : 86.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.80 (0.23), residues: 1194 helix: 0.33 (0.34), residues: 226 sheet: -1.21 (0.36), residues: 216 loop : -2.95 (0.21), residues: 752 ********************** 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 179 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1993 time to fit residues: 51.6353 Evaluate side-chains 147 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.042 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4898 ------------------------------------------------------------------------------- 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: 0.9980 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 chunk 17 optimal weight: 0.2980 chunk 83 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.183252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.155244 restraints weight = 26531.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.156774 restraints weight = 16375.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.157154 restraints weight = 12370.169| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 9553 Z= 0.191 Angle : 0.680 11.157 12992 Z= 0.358 Chirality : 0.046 0.189 1465 Planarity : 0.005 0.044 1689 Dihedral : 6.166 49.986 1296 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.34 % Allowed : 12.65 % Favored : 87.02 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -2.65 (0.24), residues: 1194 helix: 0.42 (0.35), residues: 226 sheet: -1.05 (0.37), residues: 210 loop : -2.86 (0.21), residues: 758 =============================================================================== Job complete usr+sys time: 2005.59 seconds wall clock time: 37 minutes 26.87 seconds (2246.87 seconds total)